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<h1 id="index">Index</h1>

<div class="genindex-jumpbox">
 <a href="#Symbols"><strong>Symbols</strong></a>
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</div>
<h2 id="Symbols">Symbols</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    -a &lt;author&gt;

      <ul>
        <li><a href="f90doc.html#cmdoption-f90doc-a">f90doc command line option</a>
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    -i &lt;intro&gt;

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        <li><a href="f90doc.html#cmdoption-f90doc-i">f90doc command line option</a>
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    -l

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        <li><a href="f90doc.html#cmdoption-f90doc-l">f90doc command line option</a>
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        <li><a href="f90doc.html#cmdoption-f90doc-n">f90doc command line option</a>
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    -t &lt;title&gt;

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        <li><a href="f90doc.html#cmdoption-f90doc-t">f90doc command line option</a>
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<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="io.html#quippy.nmwiz.NMDWriter.__init__">__init__() (quippy.nmwiz.NMDWriter method)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._arrays">_arrays (quippy.oo_fortran.FortranDerivedType attribute)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._elements">_elements (quippy.oo_fortran.FortranDerivedType attribute)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._fpointer">_fpointer (quippy.oo_fortran.FortranDerivedType attribute)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._get_array_shape">_get_array_shape() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._interfaces">_interfaces (quippy.oo_fortran.FortranDerivedType attribute)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._routines">_routines (quippy.oo_fortran.FortranDerivedType attribute)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._runinterface">_runinterface() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._runroutine">_runroutine() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._subobjs">_subobjs (quippy.oo_fortran.FortranDerivedType attribute)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType._update">_update() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="system.html#quippy.system.a2s">a2s() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.abort_on_mpi_error">abort_on_mpi_error() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.activate">activate() (quippy.system.InOutput method)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.active">active (quippy.system.InOutput attribute)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.add_array">add_array() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.add_atoms">add_atoms() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.add_atoms">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      </ul></li>
      <li><a href="connection.html#quippy.atoms.Connection.add_bond">add_bond() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.add_constraint">add_constraint() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.add_cut_hydrogens">add_cut_hydrogens() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.add_identity">add_identity() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.add_identity">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.add_identity">[2]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.add_property">add_property() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">add_property_from_pointer() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.add_thermostat">add_thermostat() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.add_thermostat">(quippy.dynamicalsystem.Dynamics method)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.add_thermostats">add_thermostats() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="lotf.html#quippy.adjustablepotential.adjustable_potential_finalise">adjustable_potential_finalise() (in module quippy.adjustablepotential)</a>
</li>
      <li><a href="lotf.html#quippy.adjustablepotential.adjustable_potential_force">adjustable_potential_force() (in module quippy.adjustablepotential)</a>
</li>
      <li><a href="lotf.html#quippy.adjustablepotential.adjustable_potential_init">adjustable_potential_init() (in module quippy.adjustablepotential)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.advance">advance() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.advance">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.advance">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.advance_verlet">advance_verlet() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="lotf.html#quippy.lotf.LOTFDynamics.advance_verlet">(quippy.lotf.LOTFDynamics method)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.advance_verlet1">advance_verlet1() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.advance_verlet2">advance_verlet2() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.align">align() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.all">all() (quippy.farray.FortranArray method)</a>

      <ul>
        <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.all">(quippy.mpi_context.MPI_context method)</a>
</li>
      </ul></li>
      <li><a href="system.html#quippy.system.alloc_trace">alloc_trace() (in module quippy.system)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.allocate">allocate() (quippy.atoms.DomainDecomposition method)</a>

      <ul>
        <li><a href="table.html#quippy.table.Table.allocate">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.alpha_quartz">alpha_quartz() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.alpha_quartz_cubic">alpha_quartz_cubic() (in module quippy.structures)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.amend_constraint">amend_constraint() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="util.html#quippy.util.analyse_timings">analyse_timings() (in module quippy.util)</a>
</li>
      <li><a href="structures.html#quippy.structures.anatase_cubic">anatase_cubic() (in module quippy.structures)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.angle">angle() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="structures.html#quippy.structures.angle_between">angle_between() (in module quippy.structures)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.angular_momentum">angular_momentum() (in module quippy.dynamicalsystem)</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.angular_momentum">[1]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.angular_momentum">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.angular_momentum">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      </ul></li>
      <li><a href="simplex.html#quippy.simplex.DownhillSimplex.anneal_step">anneal_step() (quippy.simplex.DownhillSimplex method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.any">any() (quippy.farray.FortranArray method)</a>

      <ul>
        <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.any">(quippy.mpi_context.MPI_context method)</a>
</li>
      </ul></li>
      <li><a href="crack.html#quippy.crack.CrackParams.any_per_atom_tau">any_per_atom_tau() (quippy.crack.CrackParams method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.append">append() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="table.html#quippy.table.Table.append">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="table.html#quippy.table.Table.append_column">append_column() (quippy.table.Table method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="cp2k.html#quippy.cp2k.apply_cp2k_sort_order">apply_cp2k_sort_order() (in module quippy.cp2k)</a>
</li>
      <li><a href="crack.html#quippy.crack.ConstantStrainRate.apply_strain">apply_strain() (quippy.crack.ConstantStrainRate method)</a>
</li>
      <li><a href="structures.html#quippy.structures.arbitrary_supercell">arbitrary_supercell() (in module quippy.structures)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.argmax">argmax() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.argmin">argmin() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="util.html#quippy.util.args_str">args_str() (in module quippy.util)</a>
</li>
      <li><a href="util.html#quippy.util.args_str_to_dict">args_str_to_dict() (in module quippy.util)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.argsort">argsort() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.arrays">arrays (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.arrays_lt">arrays_lt() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="io.html#module-ase.io.extxyz">ase.io.extxyz (module)</a>
</li>
      <li><a href="electrostaticembed.html#quippy.electrostaticembed.assign_grid_coordinates">assign_grid_coordinates() (in module quippy.electrostaticembed)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.assignment">assignment() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.assignment">(quippy.atoms.Connection method)</a>
</li>
        <li><a href="dictionary.html#quippy.dictionary.Dictionary.assignment">(quippy.dictionary.Dictionary method)</a>
</li>
        <li><a href="quaternions.html#quippy.quaternions.Quaternion.assignment">(quippy.quaternions.Quaternion method)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#module-atomeye">atomeye (module)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer">AtomEyeViewer (class in atomeye)</a>
</li>
      <li><a href="io.html#quippy.atomeyewriter.AtomEyeWriter">AtomEyeWriter (class in quippy.atomeyewriter)</a>
</li>
      <li><a href="periodictable.html#quippy.periodictable.atomic_number">atomic_number() (in module quippy.periodictable)</a>, <a href="periodictable.html#quippy.periodictable.atomic_number">[1]</a>, <a href="periodictable.html#quippy.periodictable.atomic_number">[2]</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.atomic_strain">atomic_strain() (in module quippy.elasticity)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.AtomResolvedStressField">AtomResolvedStressField (class in quippy.elasticity)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.atoms">atoms (atomeye.AtomEyeViewer attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms">Atoms (class in quippy.atoms)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.add_atoms">Atoms.add_atoms() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.add_atoms">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.add_atoms">[2]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">Atoms.add_property_from_pointer() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">[2]</a>, <a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">[3]</a>, <a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">[4]</a>, <a href="atoms.html#quippy.atoms.Atoms.add_property_from_pointer">[5]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.diff_min_image">Atoms.diff_min_image() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.diff_min_image">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.diff_min_image">[2]</a>, <a href="atoms.html#quippy.atoms.Atoms.diff_min_image">[3]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.distance_min_image">Atoms.distance_min_image() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.distance_min_image">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.distance_min_image">[2]</a>, <a href="atoms.html#quippy.atoms.Atoms.distance_min_image">[3]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_param_value">Atoms.get_param_value() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[2]</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[3]</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[4]</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[5]</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[6]</a>, <a href="atoms.html#quippy.atoms.Atoms.get_param_value">[7]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.remove_atoms">Atoms.remove_atoms() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.remove_atoms">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.remove_atoms">[2]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_atoms">Atoms.set_atoms() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.set_atoms">[1]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_param_value">Atoms.set_param_value() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.Atoms.set_param_value">[1]</a>, <a href="atoms.html#quippy.atoms.Atoms.set_param_value">[2]</a>, <a href="atoms.html#quippy.atoms.Atoms.set_param_value">[3]</a>, <a href="atoms.html#quippy.atoms.Atoms.set_param_value">[4]</a>, <a href="atoms.html#quippy.atoms.Atoms.set_param_value">[5]</a>, <a href="atoms.html#quippy.atoms.Atoms.set_param_value">[6]</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.atoms_properties">atoms_properties (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="io.html#quippy.io.atoms_reader">atoms_reader() (in module quippy.io)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsList">AtomsList (class in quippy.io)</a>
</li>
      <li><a href="qlab.html#qlab.AtomsListViewer">AtomsListViewer (class in qlab)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsReader">AtomsReader (class in quippy.io)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsReaders">AtomsReaders (in module quippy.io)</a>
</li>
      <li><a href="qlab.html#qlab.AtomsReaderViewer">AtomsReaderViewer (class in qlab)</a>
</li>
      <li><a href="qlab.html#qlab.AtomsViewer">AtomsViewer (class in qlab)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsWriter">AtomsWriter() (in module quippy.io)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsWriters">AtomsWriters (in module quippy.io)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.attach">attach() (quippy.dynamicalsystem.Dynamics method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.aux_property_coloring">aux_property_coloring() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.aux_property_coloring">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.aux_property_coloring">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.average_temperature">average_temperature (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.averaging_time">averaging_time (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.avg_temp">avg_temp (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.avg_time">avg_time (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="system.html#quippy.system.InOutput.backspace">backspace() (quippy.system.InOutput method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.backward">backward() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.backward">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.backward">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="potential.html#quippy.potential.Potential.band_structure">band_structure() (quippy.potential.Potential method)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.barrier">barrier() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.bcast">bcast() (in module quippy.dictionary)</a>, <a href="dictionary.html#quippy.dictionary.bcast">[1]</a>, <a href="dictionary.html#quippy.dictionary.bcast">[2]</a>

      <ul>
        <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">(quippy.mpi_context.MPI_context method)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.bcc">bcc() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.bcc1">bcc1() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.beta_tin">beta_tin() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.beta_tin4">beta_tin4() (in module quippy.structures)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.bfs_grow_list">bfs_grow_list() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.bfs_grow_single">bfs_grow_single() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.bfs_step">bfs_step() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.binary_search">binary_search() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.binary_search">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.binary_search">[2]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.binom">binom() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.block">block (atomeye.AtomEyeViewer attribute)</a>
</li>
      <li><a href="structures.html#quippy.structures.bond_angle_mean_dev">bond_angle_mean_dev() (in module quippy.structures)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.bond_length">bond_length() (in module quippy.atoms)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k.bonds_from_avgpos">bonds_from_avgpos() (in module quippy.cp2k)</a>
</li>
      <li><a href="polarization.html#quippy.polarization.born_effective_charge">born_effective_charge() (in module quippy.polarization)</a>
</li>
      <li><a href="structures.html#quippy.structures.bulk">bulk() (in module quippy.structures)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.bulk_modulus">bulk_modulus() (quippy.potential.Potential method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.cache_invalid">cache_invalid (quippy.dictionary.Dictionary attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc">calc (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.calc">calc() (quippy.descriptors.Descriptor method)</a>

      <ul>
        <li><a href="phonons.html#quippy.phonons.Phonon_fine.calc">(quippy.phonons.Phonon_fine method)</a>
</li>
        <li><a href="potential.html#quippy.potential.Potential.calc">(quippy.potential.Potential method)</a>
</li>
      </ul></li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.calc_array">calc_array() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k_driver.calc_charge_lsd">calc_charge_lsd() (in module quippy.cp2k_driver)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc_connect">calc_connect() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.calc_connect">(quippy.atoms.Connection method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc_connect_hysteretic">calc_connect_hysteretic() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.calc_connect_hysteretic">(quippy.atoms.Connection method)</a>
</li>
      </ul></li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.calc_descriptor">calc_descriptor() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc_dists">calc_dists() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.calc_dists">(quippy.atoms.Connection method)</a>
</li>
      </ul></li>
      <li><a href="potential.html#quippy.potential.Potential.calc_elastic_constants">calc_elastic_constants() (quippy.potential.Potential method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.calc_electrostatic_potential">calc_electrostatic_potential() (quippy.potential.Potential method)</a>
</li>
      <li><a href="topology.html#quippy.topology.calc_mean_pos">calc_mean_pos() (in module quippy.topology)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc_msd">calc_msd() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc_qw">calc_qw() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.calc_qw_grad">calc_qw_grad() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.calc_tb_matrices">calc_tb_matrices() (quippy.potential.Potential method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.calculate">calculate() (quippy.potential.Potential method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.calculate_numerical_forces">calculate_numerical_forces() (quippy.potential.Potential method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.calculate_numerical_stress">calculate_numerical_stress() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.capture">capture() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.capture">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.capture">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.cart_shift">cart_shift() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.carve_cluster">carve_cluster() (in module quippy.clusters)</a>
</li>
      <li><a href="io.html#quippy.castep.CastepCell">CastepCell (class in quippy.castep)</a>
</li>
      <li><a href="io.html#quippy.castep.CastepParam">CastepParam (class in quippy.castep)</a>
</li>
      <li><a href="io.html#quippy.castep.CastepPotential">CastepPotential (class in quippy.castep)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.cell">cell (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.cell_heads">cell_heads (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.cell_n">cell_n() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.cell_of_pos">cell_of_pos() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.cell_volume">cell_volume() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.cell_volume">[1]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.cell_volume">(quippy.atoms.Atoms method)</a>
</li>
      </ul></li>
      <li><a href="connection.html#quippy.atoms.Connection.cells_initialise">cells_initialise() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.cellsna">cellsna (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.center">center (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.center">center() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.central_symmetry_coloring">central_symmetry_coloring() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.central_symmetry_coloring">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.central_symmetry_coloring">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.centre_of_mass">centre_of_mass() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.centre_on_atom_1">centre_on_atom_1() (in module quippy.real_space_covariance)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.change_atom_r_ratio">change_atom_r_ratio() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.change_atom_r_ratio">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.change_atom_r_ratio">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.change_aux_colormap">change_aux_colormap() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.change_aux_colormap">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.change_aux_colormap">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.change_aux_property_threshold">change_aux_property_threshold() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.change_aux_property_threshold">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.change_aux_property_threshold">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.change_bgcolor">change_bgcolor() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.change_bgcolor">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.change_bgcolor">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.change_bond_radius">change_bond_radius() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.change_bond_radius">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.change_bond_radius">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.change_cutting_plane_wireframe_mode">change_cutting_plane_wireframe_mode() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.change_cutting_plane_wireframe_mode">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.change_view_angle_amplification">change_view_angle_amplification() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.change_view_angle_amplification">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.change_wireframe_mode">change_wireframe_mode() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.change_wireframe_mode">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="io.html#quippy.castep.check_pspots">check_pspots() (in module quippy.castep)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.check_size">check_size() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[4]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[5]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[6]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[7]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[8]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[9]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[10]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[11]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[12]</a>, <a href="linearalgebra.html#quippy.linearalgebra.check_size">[13]</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.check_state">check_state() (quippy.potential.Potential method)</a>
</li>
      <li><a href="io.html#quippy.cinoutput.CInOutput">CInOutput (class in quippy.cinoutput)</a>
</li>
      <li><a href="io.html#quippy.cinoutput.CInOutputReader">CInOutputReader (class in quippy.cinoutput)</a>
</li>
      <li><a href="io.html#quippy.cinoutput.CInOutputWriter">CInOutputWriter (class in quippy.cinoutput)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.classical_args">classical_args (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.classical_args_str">classical_args_str (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.classical_force_reweight">classical_force_reweight (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="qlab.html#qlab.clip_visible">clip_visible() (in module qlab)</a>

      <ul>
        <li><a href="qlab.html#qlab.QuippyViewer.clip_visible">(qlab.QuippyViewer method)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.close">close() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.close">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.close">(in module qlab)</a>
</li>
        <li><a href="io.html#quippy.cinoutput.CInOutput.close">(quippy.cinoutput.CInOutput method)</a>
</li>
        <li><a href="io.html#quippy.io.AtomsReader.close">(quippy.io.AtomsReader method)</a>
</li>
        <li><a href="io.html#quippy.nmwiz.NMDWriter.close">(quippy.nmwiz.NMDWriter method)</a>
</li>
        <li><a href="system.html#quippy.system.InOutput.close">(quippy.system.InOutput method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.closest_atom">closest_atom() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="system.html#quippy.system.cmd_arg_count">cmd_arg_count() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.coalesce_in_one_periodic_image">coalesce_in_one_periodic_image() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.col_iter">col_iter() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.collect">collect() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.collect_real2">collect_real2() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.cols">cols (quippy.farray.FortranArray attribute)</a>
</li>
      <li><a href="qpxml.html#quippy.qpxml.combine_xml">combine_xml() (in module quippy.qpxml)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.comm_atoms">comm_atoms() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.comm_atoms_to_all">comm_atoms_to_all() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.comm_ghosts">comm_ghosts() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.comm_reverse">comm_reverse() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.complement">complement() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.connect">connect (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection">Connection (class in quippy.atoms)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.n_neighbours">Connection.n_neighbours() (in module quippy.atoms)</a>, <a href="connection.html#quippy.atoms.Connection.n_neighbours">[1]</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.neighbour">Connection.neighbour() (in module quippy.atoms)</a>, <a href="connection.html#quippy.atoms.Connection.neighbour">[1]</a>
</li>
      <li><a href="crack.html#quippy.crack.ConstantStrainRate">ConstantStrainRate (class in quippy.crack)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_atom_plane">constrain_atom_plane() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_bondanglecos">constrain_bondanglecos() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_bondlength">constrain_bondlength() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_bondlength_dev_pow">constrain_bondlength_dev_pow() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_bondlength_diff">constrain_bondlength_diff() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_bondlength_sq">constrain_bondlength_sq() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_gap_energy">constrain_gap_energy() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_struct_factor_like_i">constrain_struct_factor_like_i() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_struct_factor_like_mag">constrain_struct_factor_like_mag() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.constrain_struct_factor_like_r">constrain_struct_factor_like_r() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.constraints">constraints (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.construct_hysteretic_region">construct_hysteretic_region() (in module quippy.clusters)</a>
</li>
      <li><a href="farray.html#quippy.farray.convert_farray_to_ndarray">convert_farray_to_ndarray() (in module quippy.farray)</a>
</li>
      <li><a href="farray.html#quippy.farray.convert_ndarray_to_farray">convert_ndarray_to_farray() (in module quippy.farray)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.coordination_function">coordination_function() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.coordination_function">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.coordination_function">[2]</a>
</li>
      <li><a href="qlab.html#qlab.AtomsViewer.copy">copy() (qlab.AtomsViewer method)</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.copy">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="io.html#quippy.castep.CastepCell.copy">(quippy.castep.CastepCell method)</a>
</li>
        <li><a href="io.html#quippy.castep.CastepParam.copy">(quippy.castep.CastepParam method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.copy_entry">copy_entry() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.copy_from">copy_from() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.copy_properties">copy_properties() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.copy_without_connect">copy_without_connect() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.cos_cutoff_function">cos_cutoff_function() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.cosine">cosine() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.cosine_neighbour">cosine_neighbour() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.count">count() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.covariance">covariance() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k_driver.cp2k_state_change">cp2k_state_change() (in module quippy.cp2k_driver)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k.CP2KInputHeader">CP2KInputHeader (class in quippy.cp2k)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k.CP2KPotential">CP2KPotential (class in quippy.cp2k)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_align_y">crack_align_y (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_apply_initial_load">crack_apply_initial_load (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_apply_load_increment">crack_apply_load_increment() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_apply_strain_ramp">crack_apply_strain_ramp() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_bulk_filename">crack_bulk_filename (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_calc_load_field">crack_calc_load_field() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_check_coordination">crack_check_coordination() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_check_coordination_atom_type">crack_check_coordination_atom_type (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_check_coordination_boundaries">crack_check_coordination_boundaries() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_check_coordination_critical_nneigh">crack_check_coordination_critical_nneigh (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_check_coordination_region">crack_check_coordination_region (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_check_surface_coordination">crack_check_surface_coordination (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_curvature">crack_curvature (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_curved_front">crack_curved_front (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_dislo_seed">crack_dislo_seed (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_double_ended">crack_double_ended (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_edge_fix_tol">crack_edge_fix_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_element">crack_element (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_find_griffith_load">crack_find_griffith_load() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_find_surface_atoms">crack_find_surface_atoms() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_find_tip">crack_find_tip() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_find_tip_coordination">crack_find_tip_coordination() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_find_tip_local_energy">crack_find_tip_local_energy() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_find_tip_percolation">crack_find_tip_percolation() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_fix_dipoles">crack_fix_dipoles (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_fix_dipoles_tol">crack_fix_dipoles_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_fix_sides">crack_fix_sides (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_free_surfaces">crack_free_surfaces (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_front_alpha">crack_front_alpha (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_front_angle_threshold">crack_front_angle_threshold (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_front_window_size">crack_front_window_size (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_g">crack_g (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_g_increment">crack_g_increment (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_g_to_k">crack_g_to_k() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_g_to_strain">crack_g_to_strain() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_graphene_notch_height">crack_graphene_notch_height (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_graphene_notch_width">crack_graphene_notch_width (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_graphene_theta">crack_graphene_theta (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_height">crack_height (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_hybrid_calc_args">crack_hybrid_calc_args() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_initial_velocity_field">crack_initial_velocity_field (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_is_edge_atom">crack_is_edge_atom() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_is_topbottom_edge_atom">crack_is_topbottom_edge_atom() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_k_field">crack_k_field() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_k_to_g">crack_k_to_g() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_lattice_guess">crack_lattice_guess (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_load_interp_length">crack_load_interp_length (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_loading">crack_loading (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_make_seed">crack_make_seed() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_make_slab">crack_make_slab() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_measure_g">crack_measure_g() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_mm_calc_args">crack_mm_calc_args() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_name">crack_name (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_num_layers">crack_num_layers (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_parse_name">crack_parse_name() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_print">crack_print() (in module quippy.crack)</a>, <a href="crack.html#quippy.crack.crack_print">[1]</a>, <a href="crack.html#quippy.crack.crack_print">[2]</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_ramp_end_g">crack_ramp_end_g (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_ramp_length">crack_ramp_length (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_ramp_start_length">crack_ramp_start_length (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_relax_bulk">crack_relax_bulk (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_relax_loading_field">crack_relax_loading_field (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_rescale_x">crack_rescale_x (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_rescale_x_z">crack_rescale_x_z (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_seed_embed_tol">crack_seed_embed_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_seed_length">crack_seed_length (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_setup_marks">crack_setup_marks() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_slab_filename">crack_slab_filename (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_strain">crack_strain (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_strain">crack_strain() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_strain_energy_release_rate">crack_strain_energy_release_rate() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_strain_increment">crack_strain_increment (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_strain_to_g">crack_strain_to_g() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_strain_zone_width">crack_strain_zone_width (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_structure">crack_structure (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_thermostat_ramp_length">crack_thermostat_ramp_length (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_thermostat_ramp_max_tau">crack_thermostat_ramp_max_tau (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_tip_grid_size">crack_tip_grid_size (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_tip_method">crack_tip_method (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_tip_min_separation">crack_tip_min_separation (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_uniform_load">crack_uniform_load() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_update_connect">crack_update_connect() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_update_selection">crack_update_selection() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_update_selection_coordination">crack_update_selection_coordination() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.crack_update_selection_crack_front">crack_update_selection_crack_front() (in module quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_vacuum_size">crack_vacuum_size (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_width">crack_width (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_x_shift">crack_x_shift (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_y_shift">crack_y_shift (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.crack_z">crack_z (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams">CrackParams (class in quippy.crack)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.read_xml">CrackParams.read_xml() (in module quippy.crack)</a>, <a href="crack.html#quippy.crack.CrackParams.read_xml">[1]</a>
</li>
      <li><a href="clusters.html#quippy.clusters.create_cluster_info_from_mark">create_cluster_info_from_mark() (in module quippy.clusters)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.create_cluster_simple">create_cluster_simple() (in module quippy.clusters)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.create_embed_and_fit_lists">create_embed_and_fit_lists() (in module quippy.clusters)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.create_embed_and_fit_lists_from_cluster_mark">create_embed_and_fit_lists_from_cluster_mark() (in module quippy.clusters)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.create_hybrid_weights">create_hybrid_weights() (in module quippy.clusters)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.create_pos_or_list_centred_hybrid_region">create_pos_or_list_centred_hybrid_region() (in module quippy.clusters)</a>
</li>
      <li><a href="topology.html#quippy.topology.create_residue_labels_arb_pos">create_residue_labels_arb_pos() (in module quippy.topology)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.cubic_interpolate">cubic_interpolate() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.cur_temp">cur_temp (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="system.html#quippy.system.current_times">current_times() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.current_verbosity">current_verbosity() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.current_version">current_version() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.cutoff">cutoff (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.cutoff">cutoff() (quippy.descriptors.Descriptor method)</a>

      <ul>
        <li><a href="potential.html#quippy.potential.Potential.cutoff">(quippy.potential.Potential method)</a>
</li>
      </ul></li>
      <li><a href="descriptors.html#quippy.descriptors.General_monomer.cutoff_">cutoff_() (quippy.descriptors.General_monomer method)</a>

      <ul>
        <li><a href="descriptors.html#quippy.descriptors.Soap.cutoff_">(quippy.descriptors.Soap method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.cutoff_skin">cutoff_skin (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.cutting_plane">cutting_plane() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.cutting_plane">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.cutting_plane">(in module qlab)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="linearalgebra.html#quippy.linearalgebra.d2coordination_function">d2coordination_function() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.d2coordination_function">[1]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.d2poly_switch">d2poly_switch() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.d3coordination_function">d3coordination_function() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.d3coordination_function">[1]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.d3poly_switch">d3poly_switch() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.damping">damping (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="system.html#quippy.system.date_and_time_string">date_and_time_string() (in module quippy.system)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.dcoordination_function">dcoordination_function() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.dcoordination_function">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.dcoordination_function">[2]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.dcos_cutoff_function">dcos_cutoff_function() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.deactivate">deactivate() (quippy.system.InOutput method)</a>
</li>
      <li><a href="system.html#quippy.system.dealloc_trace">dealloc_trace() (in module quippy.system)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.decomposed">decomposed (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.decomposition">decomposition (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.deepcopy">deepcopy() (quippy.atoms.DomainDecomposition method)</a>

      <ul>
        <li><a href="dictionary.html#quippy.dictionary.Dictionary.deepcopy">(quippy.dictionary.Dictionary method)</a>
</li>
      </ul></li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.deepcopy_no_error">deepcopy_no_error() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="atomeye.html#atomeye.default_state">default_state (in module atomeye)</a>
</li>
      <li><a href="structures.html#quippy.structures.delaunay_reduce">delaunay_reduce() (in module quippy.structures)</a>
</li>
      <li><a href="table.html#quippy.table.Table.delete">delete() (quippy.table.Table method)</a>
</li>
      <li><a href="atomeye.html#atomeye.delete_cutting_plane">delete_cutting_plane() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.delete_cutting_plane">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="topology.html#quippy.topology.delete_metal_connects">delete_metal_connects() (in module quippy.topology)</a>
</li>
      <li><a href="table.html#quippy.table.Table.delete_multiple">delete_multiple() (quippy.table.Table method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.delta">delta (atomeye.AtomEyeViewer attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.density">density() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline.deriv">deriv() (quippy.spline.Spline method)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor">Descriptor (class in quippy.descriptors)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.descriptor_sizes">descriptor_sizes() (quippy.descriptors.Descriptor method)</a>

      <ul>
        <li><a href="descriptors.html#quippy.descriptors.General_monomer.descriptor_sizes">(quippy.descriptors.General_monomer method)</a>
</li>
        <li><a href="descriptors.html#quippy.descriptors.Soap.descriptor_sizes">(quippy.descriptors.Soap method)</a>
</li>
      </ul></li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.diag">diag() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.diag">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.diag">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.diag">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.diag">[4]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.diagonalise">diagonalise() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.diagonalise">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.diagonalise">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.diagonalise">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.diagonalise">[4]</a>
</li>
      <li><a href="structures.html#quippy.structures.diamond">diamond() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.diamond2">diamond2() (in module quippy.structures)</a>
</li>
      <li><a href="util.html#quippy.util.dict_to_args_str">dict_to_args_str() (in module quippy.util)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary">Dictionary (class in quippy.dictionary)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.add_array">Dictionary.add_array() (in module quippy.dictionary)</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[1]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[2]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[3]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[4]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[5]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[6]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[7]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[8]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[9]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[10]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[11]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.add_array">[12]</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.set_value">Dictionary.set_value() (in module quippy.dictionary)</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[1]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[2]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[3]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[4]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[5]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[6]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[7]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[8]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[9]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[10]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[11]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[12]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[13]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value">[14]</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">Dictionary.set_value_pointer() (in module quippy.dictionary)</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">[1]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">[2]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">[3]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">[4]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">[5]</a>, <a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">[6]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.diff">diff() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.diff_min_image">diff_min_image() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.dimensions">dimensions() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.direction_cosines">direction_cosines() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.direction_cosines_min_image">direction_cosines_min_image() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.directionality">directionality() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.disable">disable() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.disable_damping">disable_damping() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="system.html#quippy.system.disable_timing">disable_timing() (in module quippy.system)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.discard_non_min_images">discard_non_min_images() (in module quippy.clusters)</a>
</li>
      <li><a href="structures.html#quippy.structures.disloc_noam">disloc_noam() (in module quippy.structures)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.display">display() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.display">(in module atomeye)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.distance">distance() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.distance_min_image">distance_min_image() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.distance_relative_velocity">distance_relative_velocity() (in module quippy.dynamicalsystem)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.distances">distances() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.divide_cell">divide_cell() (in module quippy.atoms)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k_driver.do_cp2k_calc">do_cp2k_calc() (in module quippy.cp2k_driver)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.do_output">do_output() (quippy.system.InOutput method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.domain">domain (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition">DomainDecomposition (class in quippy.atoms)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.doverlap_func">doverlap_func() (in module quippy.real_space_covariance)</a>
</li>
      <li><a href="simplex.html#quippy.simplex.DownhillSimplex">DownhillSimplex (class in quippy.simplex)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.dpoly_switch">dpoly_switch() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.draw_arrows">draw_arrows() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.draw_arrows">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.draw_arrows">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.drotmat_dquaternion">drotmat_dquaternion() (in module quippy.real_space_covariance)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.dt">dt (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.dw">dw (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="phonons.html#quippy.phonons.dynamical_matrix_solve">dynamical_matrix_solve() (in module quippy.phonons)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem">DynamicalSystem (class in quippy.dynamicalsystem)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.add_atoms">DynamicalSystem.add_atoms() (in module quippy.dynamicalsystem)</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.add_atoms">[1]</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.remove_atoms">DynamicalSystem.remove_atoms() (in module quippy.dynamicalsystem)</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.remove_atoms">[1]</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics">Dynamics (class in quippy.dynamicalsystem)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.echo">echo (atomeye.AtomEyeViewer attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.edit">edit() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.einstein_frequencies">einstein_frequencies() (in module quippy.elasticity)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.ekin">ekin (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.elastic_constants">elastic_constants() (in module quippy.elasticity)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.elastic_fields">elastic_fields() (in module quippy.elasticity)</a>, <a href="elasticity.html#quippy.elasticity.elastic_fields">[1]</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.elastic_fields_fortran">elastic_fields_fortran() (in module quippy.elasticity)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.enable">enable() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.enable_damping">enable_damping() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="system.html#quippy.system.enable_timing">enable_timing() (in module quippy.system)</a>
</li>
      <li>
    environment variable

      <ul>
        <li><a href="Tutorials/adglass.html#index-2">PATH</a>, <a href="Tutorials/adglass.html#index-3">[1]</a>, <a href="adglass.html#index-2">[2]</a>, <a href="adglass.html#index-3">[3]</a>
</li>
        <li><a href="Tutorials/adglass.html#index-0">QUIP_ARCH</a>, <a href="adglass.html#index-0">[1]</a>, <a href="install.html#index-0">[2]</a>
</li>
        <li><a href="Tutorials/adglass.html#index-1">QUIP_ROOT</a>, <a href="adglass.html#index-1">[1]</a>, <a href="install.html#index-1">[2]</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.epot">epot (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="polarization.html#quippy.polarization.epsilon_infty">epsilon_infty() (in module quippy.polarization)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.equivalent">equivalent() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.estimate_origin_extent">estimate_origin_extent() (in module quippy.clusters)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.euler_rotate">euler_rotate() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="phonons.html#quippy.phonons.eval_frozen_phonon">eval_frozen_phonon() (in module quippy.phonons)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.expand_string">expand_string() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.ext_energy">ext_energy (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.extend">extend() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="electrostaticembed.html#quippy.electrostaticembed.extent_to_ngrid">extent_to_ngrid() (in module quippy.electrostaticembed)</a>
</li>
      <li><a href="simplex.html#quippy.simplex.DownhillSimplex.extrapolate">extrapolate() (quippy.simplex.DownhillSimplex method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.extrapolate_steps">extrapolate_steps (quippy.lotf.LOTFDynamics attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="farray.html#quippy.farray.f2n">f2n() (in module quippy.farray)</a>
</li>
      <li><a href="f2py_wrapper_gen.html#module-f2py_wrapper_gen">f2py_wrapper_gen (module)</a>
</li>
      <li><a href="f90doc.html#module-f90doc">f90doc (module)</a>
</li>
      <li>
    f90doc command line option

      <ul>
        <li><a href="f90doc.html#cmdoption-f90doc-a">-a &lt;author&gt;</a>
</li>
        <li><a href="f90doc.html#cmdoption-f90doc-i">-i &lt;intro&gt;</a>
</li>
        <li><a href="f90doc.html#cmdoption-f90doc-l">-l</a>
</li>
        <li><a href="f90doc.html#cmdoption-f90doc-n">-n</a>
</li>
        <li><a href="f90doc.html#cmdoption-f90doc-s">-s</a>
</li>
        <li><a href="f90doc.html#cmdoption-f90doc-t">-t &lt;title&gt;</a>
</li>
      </ul></li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.factorial">factorial() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.factorial2">factorial2() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.factorial_int">factorial_int() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.fake_smooth_pos">fake_smooth_pos() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="farray.html#quippy.farray.farray">farray() (in module quippy.farray)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc">fcc() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc1">fcc1() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc_11b2_edge_disloc">fcc_11b2_edge_disloc() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc_disloc_malc">fcc_disloc_malc() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc_z100">fcc_z100() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc_z111">fcc_z111() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.fcc_z111_ortho">fcc_z111_ortho() (in module quippy.structures)</a>
</li>
      <li><a href="farray.html#quippy.farray.fenumerate">fenumerate() (in module quippy.farray)</a>
</li>
      <li><a href="farray.html#quippy.farray.fidentity">fidentity() (in module quippy.farray)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.filename_initialise">filename_initialise() (quippy.potential.Potential method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.fill">fill() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.fill_random_integer">fill_random_integer() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsReader.filter">filter() (quippy.io.AtomsReader method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.find">find() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.find">[1]</a>

      <ul>
        <li><a href="table.html#quippy.table.Table.find">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="topology.html#quippy.topology.find_a2_monomer">find_a2_monomer() (in module quippy.topology)</a>
</li>
      <li><a href="topology.html#quippy.topology.find_ab_monomer">find_ab_monomer() (in module quippy.topology)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.find_atom">find_atom() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.find_atom">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.find_atom">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.find_closest">find_closest() (in module quippy.structures)</a>
</li>
      <li><a href="system.html#quippy.system.find_closing_delimiter">find_closing_delimiter() (in module quippy.system)</a>
</li>
      <li><a href="structures.html#quippy.structures.find_compatible_supercells">find_compatible_supercells() (in module quippy.structures)</a>
</li>
      <li><a href="crack.html#quippy.crack.find_crack_tip_coordination">find_crack_tip_coordination() (in module quippy.crack)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="crack.html#quippy.crack.find_crack_tip_stress_field">find_crack_tip_stress_field() (in module quippy.crack)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.find_in_array">find_in_array() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.find_in_array">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.find_in_array">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.find_in_array">[3]</a>
</li>
      <li><a href="structures.html#quippy.structures.find_motif">find_motif() (in module quippy.structures)</a>
</li>
      <li><a href="topology.html#quippy.topology.find_motif_backbone">find_motif_backbone() (in module quippy.topology)</a>
</li>
      <li><a href="topology.html#quippy.topology.find_water_monomer">find_water_monomer() (in module quippy.topology)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.first">first() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.first">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.first">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="connection.html#quippy.atoms.fit_box_in_cell">fit_box_in_cell() (in module quippy.atoms)</a>
</li>
      <li><a href="crack.html#quippy.crack.fit_crack_stress_field">fit_crack_stress_field() (in module quippy.crack)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.fit_cubic">fit_cubic() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.fit_elastic_constants">fit_elastic_constants() (in module quippy.elasticity)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.fit_forces">fit_forces() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.fit_hops">fit_hops (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.fit_method">fit_method (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.fit_spring_hops">fit_spring_hops (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.fixed_size">fixed_size (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="atomeye.html#atomeye.flip_cutting_plane">flip_cutting_plane() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.flip_cutting_plane">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="crack.html#quippy.crack.CrackParams.force_integration_end_file">force_integration_end_file (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.force_integration_n_steps">force_integration_n_steps (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="potential.html#quippy.potential.force_test">force_test() (in module quippy.potential)</a>
</li>
      <li><a href="potential.html#quippy.potential.ForceMixingPotential">ForceMixingPotential (class in quippy.potential)</a>
</li>
      <li><a href="fortranio.html#quippy.fortranio.fortran_print">fortran_print() (in module quippy.fortranio)</a>
</li>
      <li><a href="fortranio.html#quippy.fortranio.fortran_print_error">fortran_print_error() (in module quippy.fortranio)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray">FortranArray (class in quippy.farray)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType">FortranDerivedType (class in quippy.oo_fortran)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedTypes">FortranDerivedTypes (in module quippy.oo_fortran)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.forward">forward() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.forward">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.forward">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.frame">frame (atomeye.AtomEyeViewer attribute)</a>, <a href="atomeye.html#atomeye.AtomEyeViewer.frame">[1]</a>
</li>
      <li><a href="farray.html#quippy.farray.frange">frange() (in module quippy.farray)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.free_context">free_context() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.frobenius_norm">frobenius_norm() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="table.html#quippy.table.Table.from_atom_indices">from_atom_indices() (quippy.table.Table class method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.from_atom_list">from_atom_list() (quippy.table.Table class method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.from_atom_mask">from_atom_mask() (quippy.table.Table class method)</a>
</li>
      <li><a href="farray.html#quippy.farray.fvar">fvar() (in module quippy.farray)</a>
</li>
      <li><a href="farray.html#quippy.farray.fzeros">fzeros() (in module quippy.farray)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.g">g (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.G_to_strain">G_to_strain() (in module quippy.crack)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.gaussian_velocity_component">gaussian_velocity_component() (in module quippy.dynamicalsystem)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.gcat">gcat() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="qlab.html#qlab.gcat">(in module qlab)</a>
</li>
        <li><a href="qlab.html#qlab.AtomsViewer.gcat">(qlab.AtomsViewer method)</a>
</li>
      </ul></li>
      <li><a href="qlab.html#qlab.gcv">gcv() (in module qlab)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.General_monomer">General_monomer (class in quippy.descriptors)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get">get() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_all_distances">get_all_distances() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_angle">get_angle() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_angles">get_angles() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_angular_momentum">get_angular_momentum() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_array">get_array() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="dictionary.html#quippy.dictionary.Dictionary.get_array">(quippy.dictionary.Dictionary method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_atom">get_atom() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_atomic_numbers">get_atomic_numbers() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="structures.html#quippy.structures.get_bond_lengths">get_bond_lengths() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.get_bulk_params">get_bulk_params() (in module quippy.structures)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get_calc_args">get_calc_args() (quippy.potential.Potential method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get_calc_args_str">get_calc_args_str() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_calculator">get_calculator() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_cell">get_cell() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_cell_lengths_and_angles">get_cell_lengths_and_angles() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_celldisp">get_celldisp() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_center_of_mass">get_center_of_mass() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_charges">get_charges() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_chemical_formula">get_chemical_formula() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_chemical_symbols">get_chemical_symbols() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="system.html#quippy.system.get_cmd_arg">get_cmd_arg() (in module quippy.system)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.get_damping_time">get_damping_time() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get_default_properties">get_default_properties() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atomeye.html#atomeye.get_delta">get_delta() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.get_delta">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_dihedral">get_dihedral() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_dipole_moment">get_dipole_moment() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_distance">get_distance() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_distances">get_distances() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get_elastic_constants">get_elastic_constants() (quippy.potential.Potential method)</a>
</li>
      <li><a href="crack.html#quippy.crack.get_energy_release_rate">get_energy_release_rate() (in module quippy.crack)</a>
</li>
      <li><a href="system.html#quippy.system.get_env_var">get_env_var() (in module quippy.system)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.get_extrapolation_forces">get_extrapolation_forces() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_forces">get_forces() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.get_frame">get_frame() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.get_frame">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="qpxml.html#quippy.qpxml.get_gap_version">get_gap_version() (in module quippy.qpxml)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.get_hybrid_list">get_hybrid_list() (in module quippy.clusters)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_initial_charges">get_initial_charges() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_initial_magnetic_moments">get_initial_magnetic_moments() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.get_interpolation_forces">get_interpolation_forces() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.get_key">get_key() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_kinetic_energy">get_kinetic_energy() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.get_lattice_params">get_lattice_params() (in module quippy.atoms)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_magnetic_moment">get_magnetic_moment() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_magnetic_moments">get_magnetic_moments() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="potential.html#quippy.potential.Potential.get_magnetic_moments">(quippy.potential.Potential method)</a>
</li>
      </ul></li>
      <li><a href="system.html#quippy.system.get_mainlog_errorlog_ptr">get_mainlog_errorlog_ptr() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_masses">get_masses() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.get_min_max_images">get_min_max_images() (in module quippy.atoms)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_momenta">get_momenta() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_moments_of_inertia">get_moments_of_inertia() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="system.html#quippy.system.get_mpi_size_rank">get_mpi_size_rank() (in module quippy.system)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.get_neighbors">get_neighbors() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.get_neighbours">get_neighbours() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_number_of_atoms">get_number_of_atoms() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.get_number_of_steps">get_number_of_steps() (quippy.lotf.LOTFDynamics method)</a>

      <ul>
        <li><a href="potential.html#quippy.potential.Minim.get_number_of_steps">(quippy.potential.Minim method)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.get_number_of_thermostats">get_number_of_thermostats() (quippy.dynamicalsystem.Dynamics method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get_numeric_forces">get_numeric_forces() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_param_value">get_param_value() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_pbc">get_pbc() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_positions">get_positions() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_potential_energies">get_potential_energies() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="potential.html#quippy.potential.Potential.get_potential_energies">(quippy.potential.Potential method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_potential_energy">get_potential_energy() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="potential.html#quippy.potential.ForceMixingPotential.get_qm_atoms">get_qm_atoms() (quippy.potential.ForceMixingPotential method)</a>
</li>
      <li><a href="system.html#quippy.system.get_quippy_running">get_quippy_running() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_reciprocal_cell">get_reciprocal_cell() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.get_reference_forces">get_reference_forces() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_scaled_positions">get_scaled_positions() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.get_size_angstrom">get_size_angstrom() (atomeye.AtomEyeViewer method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.get_size_pixels">get_size_pixels() (atomeye.AtomEyeViewer method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.get_state">get_state() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="crack.html#quippy.crack.get_strain">get_strain() (in module quippy.crack)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_stress">get_stress() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="elasticity.html#quippy.elasticity.AtomResolvedStressField.get_stress">(quippy.elasticity.AtomResolvedStressField method)</a>
</li>
      </ul></li>
      <li><a href="crack.html#quippy.crack.get_stress_intensity_factor">get_stress_intensity_factor() (in module quippy.crack)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_stresses">get_stresses() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="elasticity.html#quippy.elasticity.AtomResolvedStressField.get_stresses">(quippy.elasticity.AtomResolvedStressField method)</a>
</li>
        <li><a href="potential.html#quippy.potential.Potential.get_stresses">(quippy.potential.Potential method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_tags">get_tags() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_temperature">get_temperature() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.get_thermostat_temperatures">get_thermostat_temperatures() (quippy.dynamicalsystem.Dynamics method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.get_time">get_time() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="system.html#quippy.system.get_timing">get_timing() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_total_energy">get_total_energy() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.get_type">get_type() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.get_type_and_size">get_type_and_size() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.get_unrelaxed_elastic_constants">get_unrelaxed_elastic_constants() (quippy.potential.Potential method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.get_value">get_value() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_velocities">get_velocities() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="qlab.html#qlab.get_viewer">get_viewer() (in module qlab)</a>
</li>
      <li><a href="qlab.html#qlab.get_viewer_names">get_viewer_names() (in module qlab)</a>
</li>
      <li><a href="qlab.html#qlab.get_viewers">get_viewers() (in module qlab)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.get_visible">get_visible() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="qlab.html#qlab.get_visible">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.get_volume">get_volume() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.ghost_properties">ghost_properties (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.ghosts_l">ghosts_l (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.ghosts_r">ghosts_r (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.global_to_local">global_to_local (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="structures.html#quippy.structures.graphene_cubic">graphene_cubic() (in module quippy.structures)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.graphene_elastic">graphene_elastic() (in module quippy.elasticity)</a>
</li>
      <li><a href="structures.html#quippy.structures.graphene_sheet">graphene_sheet() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.graphene_slab">graphene_slab() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.graphene_tube">graphene_tube() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.graphite">graphite() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.graphite_rhombohedral">graphite_rhombohedral() (in module quippy.structures)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="H">H</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="crack.html#quippy.crack.CrackParams.hack_fit_on_eqm_coordination_only">hack_fit_on_eqm_coordination_only (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.hack_qm_zero_z_force">hack_qm_zero_z_force (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.has">has() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.has_key">has_key() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.has_property">has_property() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.hat">hat() (quippy.farray.FortranArray method)</a>

      <ul>
        <li><a href="structures.html#quippy.structures.MillerIndex.hat">(quippy.structures.MillerIndex method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="structures.html#quippy.structures.hcp">hcp() (in module quippy.structures)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.heap_sort">heap_sort() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.heap_sort">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.heap_sort">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.heap_sort">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.heap_sort">[4]</a>
</li>
      <li><a href="system.html#quippy.system.hello_world">hello_world() (in module quippy.system)</a>
</li>
      <li><a href="qlab.html#qlab.highlight_qm_region">highlight_qm_region() (in module qlab)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.histogram">histogram() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.histogram">[1]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.hysteretic_connect">hysteretic_connect (quippy.atoms.Atoms attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="structures.html#quippy.structures.imma">imma() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.imma4">imma4() (in module quippy.structures)</a>
</li>
      <li><a href="crack.html#quippy.crack.in_ellipse">in_ellipse() (in module quippy.crack)</a>
</li>
      <li><a href="system.html#quippy.system.increase_stack">increase_stack() (in module quippy.system)</a>
</li>
      <li><a href="table.html#quippy.table.Table.increment">increment (quippy.table.Table attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.index_to_z_index">index_to_z_index() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.indices">indices (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="util.html#quippy.util.infer_format">infer_format() (in module quippy.util)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.info">info (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.initialise_adjustable_potential">initialise_adjustable_potential() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput">InOutput (class in quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.read_ascii">InOutput.read_ascii() (in module quippy.system)</a>, <a href="system.html#quippy.system.InOutput.read_ascii">[1]</a>
</li>
      <li><a href="table.html#quippy.table.Table.insert">insert() (quippy.table.Table method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.insert_observer">insert_observer() (quippy.dynamicalsystem.Dynamics method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.insertion_sort">insertion_sort() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.insertion_sort">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.insertion_sort">[2]</a>
</li>
      <li><a href="table.html#quippy.table.Table.int">int (quippy.table.Table attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.int_array_ge">int_array_ge() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.int_array_gt">int_array_gt() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.int_array_lt">int_array_lt() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="system.html#quippy.system.int_format_length">int_format_length() (in module quippy.system)</a>
</li>
      <li><a href="table.html#quippy.table.Table.int_part">int_part() (quippy.table.Table method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.int_subtable">int_subtable() (quippy.table.Table method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.integerdigits">integerdigits() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="table.html#quippy.table.Table.intsize">intsize (quippy.table.Table attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.inverse">inverse() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.inverse">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.inverse">[2]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.inverse_svd_threshold">inverse_svd_threshold() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.invsqrt_real_array1d">invsqrt_real_array1d() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_backup">io_backup (quippy.crack.CrackParams attribute)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="crack.html#quippy.crack.CrackParams.io_checkpoint_interval">io_checkpoint_interval (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_checkpoint_path">io_checkpoint_path (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_mpi_print_all">io_mpi_print_all (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_netcdf">io_netcdf (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_print_all_properties">io_print_all_properties (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_print_interval">io_print_interval (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_print_properties">io_print_properties (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_timing">io_timing (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.io_verbosity">io_verbosity (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.irwin_modeI_crack_tip_stress_field">irwin_modeI_crack_tip_stress_field() (in module quippy.crack)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.is_damping_enabled">is_damping_enabled() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.is_diagonal">is_diagonal() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.is_domain_decomposed">is_domain_decomposed() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="system.html#quippy.system.is_file_readable">is_file_readable() (in module quippy.system)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.is_in_array">is_in_array() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.is_initialised">is_initialised() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="util.html#quippy.util.is_interactive_shell">is_interactive_shell() (in module quippy.util)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.is_min_image">is_min_image (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.is_min_image">is_min_image() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.is_nearest_neighbour">is_nearest_neighbour() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.is_nearest_neighbour_abs_index">is_nearest_neighbour_abs_index() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.is_orthogonal">is_orthogonal() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_orthogonal">[1]</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType.is_same_fortran_object">is_same_fortran_object() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.is_square">is_square() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_square">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_square">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_square">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_square">[4]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.is_symmetric">is_symmetric() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_symmetric">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_symmetric">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.is_symmetric">[3]</a>
</li>
      <li><a href="lotf.html#quippy.lotf.iter_atom_centered_clusters">iter_atom_centered_clusters() (in module quippy.lotf)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.iteratoms">iteratoms() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsReader.iterframes">iterframes() (quippy.io.AtomsReader method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.iterneighbours">iterneighbours() (quippy.atoms.Connection method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.key">key() (atomeye.AtomEyeViewer method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.key_cache_invalid">key_cache_invalid (quippy.dictionary.Dictionary attribute)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.keys">keys() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.kinetic_energy">kinetic_energy() (in module quippy.dynamicalsystem)</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.kinetic_energy">[1]</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.kinetic_energy">[2]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.kinetic_energy">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.kinetic_energy">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.kinetic_virial">kinetic_virial() (in module quippy.dynamicalsystem)</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.kinetic_virial">[1]</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.kinetic_virial">[2]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.kinetic_virial">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.kinetic_virial">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      </ul></li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.kmeans">kmeans() (in module quippy.linearalgebra)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.l">l (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="find_surface_atoms.html#quippy.find_surface_atoms.label_surface_atoms">label_surface_atoms() (in module quippy.find_surface_atoms)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.last">last() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.last">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.last">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="connection.html#quippy.atoms.Connection.last_connect_cutoff">last_connect_cutoff (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.last_connect_lattice">last_connect_lattice (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.last_connect_pos">last_connect_pos (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="structures.html#quippy.structures.MillerIndex.latex">latex() (quippy.structures.MillerIndex method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.lattice">lattice (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.linear_interpolate">linear_interpolate() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="system.html#quippy.system.linebreak_string">linebreak_string() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.linebreak_string_length">linebreak_string_length() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.link_run_directory">link_run_directory() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.list_matching_prop">list_matching_prop() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.load_atom_color">load_atom_color() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.load_atom_color">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.load_atom_color">(in module qlab)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.load_aux">load_aux() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.load_aux">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.load_aux">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.load_script">load_script() (atomeye.AtomEyeViewer method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.logical">logical (quippy.table.Table attribute)</a>
</li>
      <li><a href="table.html#quippy.table.Table.logical_part">logical_part() (quippy.table.Table method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.logicalsize">logicalsize (quippy.table.Table attribute)</a>
</li>
      <li><a href="atomeye.html#atomeye.look_at_the_anchor">look_at_the_anchor() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.look_at_the_anchor">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.lookup_entry_i">lookup_entry_i() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics">LOTFDynamics (class in quippy.lotf)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.lower">lower (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="system.html#quippy.system.lower_case">lower_case() (in module quippy.system)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.lower_with_border">lower_with_border (quippy.atoms.DomainDecomposition attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.make_convex">make_convex() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="crack.html#quippy.crack.make_crack_advance_map">make_crack_advance_map() (in module quippy.crack)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.make_hermitian">make_hermitian() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.make_hermitian">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.make_hermitian">[2]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.make_lattice">make_lattice() (in module quippy.atoms)</a>
</li>
      <li><a href="system.html#quippy.system.make_run_directory">make_run_directory() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.map_into_cell">map_into_cell() (in module quippy.atoms)</a>, <a href="atoms.html#quippy.atoms.map_into_cell">[1]</a>, <a href="atoms.html#quippy.atoms.map_into_cell">[2]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.map_into_cell">(quippy.atoms.Atoms method)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.map_nearest_atoms">map_nearest_atoms() (in module quippy.structures)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.mapindices">mapindices() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.mark_cylinder">mark_cylinder() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.mark_sphere">mark_sphere() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix3x3_det">matrix3x3_det() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix3x3_inverse">matrix3x3_inverse() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix_exp">matrix_exp() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_exp">[1]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix_mvmt">matrix_mvmt() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_mvmt">[1]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix_product_sub">matrix_product_sub() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_sub">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_sub">[2]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_rl_sub">matrix_product_vect_asdiagonal_rl_sub() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_rl_sub">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_rl_sub">[2]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">matrix_product_vect_asdiagonal_sub() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[4]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[5]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[6]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[7]</a>, <a href="linearalgebra.html#quippy.linearalgebra.matrix_product_vect_asdiagonal_sub">[8]</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.max">max() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.max_cutoff">max_cutoff() (in module quippy.atoms)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline.max_knot">max_knot() (quippy.spline.Spline method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.max_length">max_length (quippy.table.Table attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.md5_hash">md5_hash() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.mean">mean() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.mem_estimate">mem_estimate() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="system.html#quippy.system.mem_info">mem_info() (in module quippy.system)</a>
</li>
      <li><a href="qpxml.html#quippy.qpxml.merge_descriptors">merge_descriptors() (in module quippy.qpxml)</a>
</li>
      <li><a href="structures.html#quippy.structures.MillerDirection">MillerDirection() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.MillerIndex">MillerIndex (class in quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.MillerPlane">MillerPlane() (in module quippy.structures)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.min">min() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline.min_knot">min_knot() (quippy.spline.Spline method)</a>
</li>
      <li><a href="structures.html#quippy.structures.min_neighbour_dist">min_neighbour_dist() (in module quippy.structures)</a>
</li>
      <li><a href="potential.html#quippy.potential.Minim">Minim (class in quippy.potential)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.minim">minim() (quippy.potential.Potential method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_eps_guess">minim_eps_guess (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_fire_dt0">minim_fire_dt0 (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_fire_dt_max">minim_fire_dt_max (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_linminroutine">minim_linminroutine (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_max_steps">minim_max_steps (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_method">minim_method (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_minimise_mm">minim_minimise_mm (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_mm_args_str">minim_mm_args_str (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_mm_eps_guess">minim_mm_eps_guess (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_mm_linminroutine">minim_mm_linminroutine (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_mm_max_steps">minim_mm_max_steps (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_mm_method">minim_mm_method (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_mm_tol">minim_mm_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_print_output">minim_print_output (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.minim_tol">minim_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="simplex.html#quippy.simplex.DownhillSimplex.minimise">minimise() (quippy.simplex.DownhillSimplex method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.moment_of_inertia_tensor">moment_of_inertia_tensor() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.momentum">momentum() (in module quippy.dynamicalsystem)</a>, <a href="dynamicalsystem.html#quippy.dynamicalsystem.momentum">[1]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.momentum">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.momentum">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      </ul></li>
      <li><a href="util.html#quippy.util.most_recent_file">most_recent_file() (in module quippy.util)</a>
</li>
      <li><a href="util.html#quippy.util.most_recent_files">most_recent_files() (in module quippy.util)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.mpi">mpi (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.mpi_all_inoutput">mpi_all_inoutput() (quippy.system.InOutput method)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context">MPI_context (class in quippy.mpi_context)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">MPI_context.bcast() (in module quippy.mpi_context)</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[1]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[2]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[3]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[4]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[5]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[6]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[7]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[8]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[9]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[10]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[11]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[12]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.bcast">[13]</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.max">MPI_context.max() (in module quippy.mpi_context)</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.max">[1]</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.min">MPI_context.min() (in module quippy.mpi_context)</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.min">[1]</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.sendrecv">MPI_context.sendrecv() (in module quippy.mpi_context)</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sendrecv">[1]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sendrecv">[2]</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.sum">MPI_context.sum() (in module quippy.mpi_context)</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum">[1]</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">MPI_context.sum_in_place() (in module quippy.mpi_context)</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[1]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[2]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[3]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[4]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[5]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[6]</a>, <a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">[7]</a>
</li>
      <li><a href="system.html#quippy.system.mpi_id">mpi_id() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.mpi_n_procs">mpi_n_procs() (in module quippy.system)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.mpi_print">mpi_print() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.mpi_setup">mpi_setup() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="clusters.html#quippy.clusters.multiple_images">multiple_images() (in module quippy.clusters)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.n">n (quippy.atoms.Atoms attribute)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.n">(quippy.atoms.Connection attribute)</a>
</li>
        <li><a href="dictionary.html#quippy.dictionary.Dictionary.n">(quippy.dictionary.Dictionary attribute)</a>
</li>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.n">(quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
        <li><a href="spline.html#quippy.spline.Spline.n">(quippy.spline.Spline attribute)</a>
</li>
        <li><a href="table.html#quippy.table.Table.n">(quippy.table.Table attribute)</a>
</li>
      </ul></li>
      <li><a href="farray.html#quippy.farray.n2f">n2f() (in module quippy.farray)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.n_dim">n_dim (quippy.descriptors.Descriptor attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.n_ghosts_l">n_ghosts_l (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.n_ghosts_r">n_ghosts_r (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.n_neighbours">n_neighbours() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.n_neighbours">(quippy.atoms.Connection method)</a>
</li>
      </ul></li>
      <li><a href="connection.html#quippy.atoms.Connection.n_neighbours_total">n_neighbours_total() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.n_perm">n_perm (quippy.descriptors.Descriptor attribute)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.n_permutations">n_permutations() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.n_recv_g_tot">n_recv_g_tot (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.n_recv_p_tot">n_recv_p_tot (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.n_send_g_tot">n_send_g_tot (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.n_send_p_tot">n_send_p_tot (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.n_test_gradient">n_test_gradient() (quippy.potential.Potential method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.n_thermostat">n_thermostat() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.nbuffer">nbuffer (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.nconstraints">nconstraints (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.ndof">ndof (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.ndomain">ndomain (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.neighbour">neighbour() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="connection.html#quippy.atoms.Connection.neighbour">(quippy.atoms.Connection method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.new_array">new_array() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.next_atom_in_cell">next_atom_in_cell (quippy.atoms.Connection attribute)</a>
</li>
      <li><a href="system.html#quippy.system.next_non_separator">next_non_separator() (in module quippy.system)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.nit_g">nit_g (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.nit_p">nit_p (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="io.html#quippy.nmwiz.NMDWriter">NMDWriter (class in quippy.nmwiz)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.nneightol">nneightol (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.nonsymmetric_diagonalise">nonsymmetric_diagonalise() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.nonsymmetric_diagonalise">[1]</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.nonzero">nonzero() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.norm">norm() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.norm">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.norm">[2]</a>

      <ul>
        <li><a href="farray.html#quippy.farray.FortranArray.norm">(quippy.farray.FortranArray method)</a>
</li>
      </ul></li>
      <li><a href="farray.html#quippy.farray.FortranArray.norm2">norm2() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.normal_coloring">normal_coloring() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.normal_coloring">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.normal_coloring">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="farray.html#quippy.farray.FortranArray.normalised">normalised() (quippy.farray.FortranArray method)</a>

      <ul>
        <li><a href="structures.html#quippy.structures.MillerIndex.normalised">(quippy.structures.MillerIndex method)</a>
</li>
      </ul></li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.normsq">normsq() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.normsq">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.normsq">[2]</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.nrestraints">nrestraints (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.nrigid">nrigid (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.nsteps">nsteps (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.ntotal">ntotal (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.number_of_constraints">number_of_constraints (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.number_of_degrees_of_freedom">number_of_degrees_of_freedom (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.number_of_lattice_vectors">number_of_lattice_vectors (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.number_of_restraints">number_of_restraints (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.number_of_rigid_bodies">number_of_rigid_bodies (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.numbers">numbers (quippy.atoms.Atoms attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomeye.html#atomeye.observer_goto">observer_goto() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.observer_goto">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.off_l">off_l (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.off_r">off_r (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="system.html#quippy.system.optional_default">optional_default() (in module quippy.system)</a>, <a href="system.html#quippy.system.optional_default">[1]</a>, <a href="system.html#quippy.system.optional_default">[2]</a>, <a href="system.html#quippy.system.optional_default">[3]</a>, <a href="system.html#quippy.system.optional_default">[4]</a>, <a href="system.html#quippy.system.optional_default">[5]</a>, <a href="system.html#quippy.system.optional_default">[6]</a>, <a href="system.html#quippy.system.optional_default">[7]</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="quaternions.html#quippy.quaternions.orientation">orientation() (in module quippy.quaternions)</a>
</li>
      <li><a href="structures.html#quippy.structures.orthorhombic_slab">orthorhombic_slab() (in module quippy.structures)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.oscillate">oscillate() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.overlap_func">overlap_func() (in module quippy.real_space_covariance)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.own_this">own_this (quippy.atoms.Atoms attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="system.html#quippy.system.pad">pad() (in module quippy.system)</a>
</li>
      <li><a href="farray.html#quippy.farray.padded_str_array">padded_str_array() (in module quippy.farray)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.pairs">pairs() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="system.html#quippy.system.parallel_print">parallel_print() (in module quippy.system)</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_check">param_check() (in module quippy.paramreader)</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_print">param_print() (in module quippy.paramreader)</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_print_help">param_print_help() (in module quippy.paramreader)</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_read_args">param_read_args() (in module quippy.paramreader)</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_read_line">param_read_line() (in module quippy.paramreader)</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_register">param_register() (in module quippy.paramreader)</a>, <a href="paramreader.html#quippy.paramreader.param_register">[1]</a>, <a href="paramreader.html#quippy.paramreader.param_register">[2]</a>, <a href="paramreader.html#quippy.paramreader.param_register">[3]</a>, <a href="paramreader.html#quippy.paramreader.param_register">[4]</a>, <a href="paramreader.html#quippy.paramreader.param_register">[5]</a>, <a href="paramreader.html#quippy.paramreader.param_register">[6]</a>, <a href="paramreader.html#quippy.paramreader.param_register">[7]</a>
</li>
      <li><a href="paramreader.html#quippy.paramreader.param_write_string">param_write_string() (in module quippy.paramreader)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.params">params (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="structures.html#quippy.structures.MillerIndex.parse">parse() (quippy.structures.MillerIndex class method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.parse_atom_mask">parse_atom_mask() (in module quippy.atoms)</a>
</li>
      <li><a href="util.html#quippy.util.parse_comma_colon_list">parse_comma_colon_list() (in module quippy.util)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.parse_line">parse_line() (quippy.system.InOutput method)</a>
</li>
      <li><a href="util.html#quippy.util.parse_params">parse_params() (in module quippy.util)</a>
</li>
      <li><a href="util.html#quippy.util.parse_slice">parse_slice() (in module quippy.util)</a>
</li>
      <li><a href="system.html#quippy.system.parse_string">parse_string() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.parse_string_orig">parse_string_orig() (in module quippy.system)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.partition_atoms">partition_atoms() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="Tutorials/adglass.html#index-2">PATH</a>, <a href="Tutorials/adglass.html#index-3">[1]</a>, <a href="adglass.html#index-2">[2]</a>, <a href="adglass.html#index-3">[3]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.pbc">pbc (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.pbc_aware_centre">pbc_aware_centre() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="crack.html#quippy.crack.percolation_step">percolation_step() (in module quippy.crack)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.periodic">periodic (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.permutation_symbol">permutation_symbol() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.permutations">permutations() (quippy.descriptors.Descriptor method)</a>
</li>
      <li><a href="phonons.html#quippy.phonons.Phonon_fine">Phonon_fine (class in quippy.phonons)</a>
</li>
      <li><a href="phonons.html#quippy.phonons.phonon_fine_calc_print">phonon_fine_calc_print() (in module quippy.phonons)</a>
</li>
      <li><a href="phonons.html#quippy.phonons.phonons_all">phonons_all() (in module quippy.phonons)</a>
</li>
      <li><a href="system.html#quippy.system.pick_up_unit">pick_up_unit() (in module quippy.system)</a>
</li>
      <li><a href="crack.html#quippy.crack.plot_stress_fields">plot_stress_fields() (in module quippy.crack)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.poisson_ratio">poisson_ratio() (in module quippy.elasticity)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.poly_switch">poly_switch() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.pop">pop() (quippy.atoms.Atoms method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.positions">positions (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential">Potential (class in quippy.potential)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.initialise">Potential.initialise() (in module quippy.potential)</a>, <a href="potential.html#quippy.potential.Potential.initialise">[1]</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.predict">predict() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.predict_2">predict_2() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.predict_3">predict_3() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="system.html#quippy.system.print_">print_() (in module quippy.system)</a>, <a href="system.html#quippy.system.print_">[1]</a>, <a href="system.html#quippy.system.print_">[2]</a>, <a href="system.html#quippy.system.print_">[3]</a>, <a href="system.html#quippy.system.print_">[4]</a>, <a href="system.html#quippy.system.print_">[5]</a>, <a href="system.html#quippy.system.print_">[6]</a>, <a href="system.html#quippy.system.print_">[7]</a>, <a href="system.html#quippy.system.print_">[8]</a>, <a href="system.html#quippy.system.print_">[9]</a>, <a href="system.html#quippy.system.print_">[10]</a>, <a href="system.html#quippy.system.print_">[11]</a>, <a href="system.html#quippy.system.print_">[12]</a>, <a href="system.html#quippy.system.print_">[13]</a>, <a href="system.html#quippy.system.print_">[14]</a>, <a href="system.html#quippy.system.print_">[15]</a>, <a href="system.html#quippy.system.print_">[16]</a>, <a href="system.html#quippy.system.print_">[17]</a>, <a href="system.html#quippy.system.print_">[18]</a>, <a href="system.html#quippy.system.print_">[19]</a>, <a href="system.html#quippy.system.print_">[20]</a>, <a href="system.html#quippy.system.print_">[21]</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.print_">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="connection.html#quippy.atoms.Connection.print_">(quippy.atoms.Connection method)</a>
</li>
        <li><a href="crack.html#quippy.crack.CrackParams.print_">(quippy.crack.CrackParams method)</a>
</li>
        <li><a href="dictionary.html#quippy.dictionary.Dictionary.print_">(quippy.dictionary.Dictionary method)</a>
</li>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.print_">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
        <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.print_">(quippy.mpi_context.MPI_context method)</a>
</li>
        <li><a href="phonons.html#quippy.phonons.Phonon_fine.print_">(quippy.phonons.Phonon_fine method)</a>
</li>
        <li><a href="potential.html#quippy.potential.Potential.print_">(quippy.potential.Potential method)</a>
</li>
        <li><a href="quaternions.html#quippy.quaternions.Quaternion.print_">(quippy.quaternions.Quaternion method)</a>
</li>
        <li><a href="spline.html#quippy.spline.Spline.print_">(quippy.spline.Spline method)</a>
</li>
        <li><a href="table.html#quippy.table.Table.print_">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.print_atom">print_atom() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="crack.html#quippy.crack.print_crack_system">print_crack_system() (in module quippy.crack)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.print_keys">print_keys() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.print_mathematica">print_mathematica() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.print_mathematica">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.print_mathematica">[2]</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.print_mem_info">print_mem_info() (quippy.system.InOutput method)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.print_mpi_id">print_mpi_id() (quippy.system.InOutput method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.print_status">print_status() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.print_thermostats">print_thermostats() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.print_thermostats">(quippy.dynamicalsystem.Dynamics method)</a>
</li>
      </ul></li>
      <li><a href="system.html#quippy.system.print_title">print_title() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.print_warning">print_warning() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.progress">progress() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.progress_timer">progress_timer() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.prop_names_string">prop_names_string() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.properties">properties (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.pseudo_inverse">pseudo_inverse() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.push_mpi_error">push_mpi_error() (in module quippy.mpi_context)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.put">put() (quippy.farray.FortranArray method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Q">Q</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="qlab.html#module-qlab">qlab (module)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_args">qm_args (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_args_str">qm_args_str (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_buffer_hops">qm_buffer_hops (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_calc_force_error">qm_calc_force_error (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_clusters">qm_clusters (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_cp2k">qm_cp2k (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_even_electrons">qm_even_electrons (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_extra_args_str">qm_extra_args_str (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_force_periodic">qm_force_periodic (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_buffer">qm_hysteretic_buffer (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_buffer_inner_radius">qm_hysteretic_buffer_inner_radius (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_buffer_nneighb_only">qm_hysteretic_buffer_nneighb_only (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_buffer_outer_radius">qm_hysteretic_buffer_outer_radius (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_connect">qm_hysteretic_connect (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_connect_cluster_radius">qm_hysteretic_connect_cluster_radius (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_connect_inner_factor">qm_hysteretic_connect_inner_factor (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_hysteretic_connect_outer_factor">qm_hysteretic_connect_outer_factor (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_little_clusters">qm_little_clusters (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_randomise_buffer">qm_randomise_buffer (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_rescale_r">qm_rescale_r (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_terminate">qm_terminate (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_transition_hops">qm_transition_hops (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.qm_vacuum_size">qm_vacuum_size (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k.qmmm_link_bonds">qmmm_link_bonds() (in module quippy.cp2k)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k_driver.qmmm_qm_abc">qmmm_qm_abc() (in module quippy.cp2k_driver)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.quasi_static_tip_move_tol">quasi_static_tip_move_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="quaternions.html#quippy.quaternions.Quaternion">Quaternion (class in quippy.quaternions)</a>
</li>
      <li><a href="quaternions.html#quippy.quaternions.Quaternion.assignment">Quaternion.assignment() (in module quippy.quaternions)</a>, <a href="quaternions.html#quippy.quaternions.Quaternion.assignment">[1]</a>
</li>
      <li><a href="Tutorials/adglass.html#index-0">QUIP_ARCH</a>, <a href="adglass.html#index-0">[1]</a>, <a href="install.html#index-0">[2]</a>
</li>
      <li><a href="io.html#quippy.cinoutput.quip_basename">quip_basename() (in module quippy.cinoutput)</a>, <a href="io.html#quippy.cinoutput.quip_basename">[1]</a>, <a href="io.html#quippy.cinoutput.quip_basename">[2]</a>
</li>
      <li><a href="io.html#quippy.cinoutput.quip_chdir">quip_chdir() (in module quippy.cinoutput)</a>, <a href="io.html#quippy.cinoutput.quip_chdir">[1]</a>, <a href="io.html#quippy.cinoutput.quip_chdir">[2]</a>
</li>
      <li><a href="io.html#quippy.cinoutput.quip_dirname">quip_dirname() (in module quippy.cinoutput)</a>, <a href="io.html#quippy.cinoutput.quip_dirname">[1]</a>, <a href="io.html#quippy.cinoutput.quip_dirname">[2]</a>
</li>
      <li><a href="io.html#quippy.cinoutput.quip_getcwd">quip_getcwd() (in module quippy.cinoutput)</a>
</li>
      <li><a href="io.html#quippy.cinoutput.quip_md5sum">quip_md5sum() (in module quippy.cinoutput)</a>
</li>
      <li><a href="Tutorials/adglass.html#index-1">QUIP_ROOT</a>, <a href="adglass.html#index-1">[1]</a>, <a href="install.html#index-1">[2]</a>
</li>
      <li><a href="util.html#quippy.util.quip_xml_parameters">quip_xml_parameters() (in module quippy.util)</a>
</li>
      <li><a href="index.html#module-quippy">quippy (module)</a>
</li>
      <li><a href="lotf.html#module-quippy.adjustablepotential">quippy.adjustablepotential (module)</a>
</li>
      <li><a href="io.html#module-quippy.asap">quippy.asap (module)</a>
</li>
      <li><a href="io.html#module-quippy.atomeyewriter">quippy.atomeyewriter (module)</a>
</li>
      <li><a href="atoms.html#module-quippy.atoms">quippy.atoms (module)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="io.html#module-quippy.castep">quippy.castep (module)</a>
</li>
      <li><a href="io.html#module-quippy.cinoutput">quippy.cinoutput (module)</a>
</li>
      <li><a href="clusters.html#module-quippy.clusters">quippy.clusters (module)</a>
</li>
      <li><a href="cp2k.html#module-quippy.cp2k">quippy.cp2k (module)</a>
</li>
      <li><a href="cp2k.html#module-quippy.cp2k_driver">quippy.cp2k_driver (module)</a>
</li>
      <li><a href="crack.html#module-quippy.crack">quippy.crack (module)</a>
</li>
      <li><a href="io.html#module-quippy.cube">quippy.cube (module)</a>
</li>
      <li><a href="io.html#module-quippy.dan">quippy.dan (module)</a>
</li>
      <li><a href="dictionary.html#module-quippy.dictionary">quippy.dictionary (module)</a>
</li>
      <li><a href="dynamicalsystem.html#module-quippy.dynamicalsystem">quippy.dynamicalsystem (module)</a>
</li>
      <li><a href="elasticity.html#module-quippy.elasticity">quippy.elasticity (module)</a>
</li>
      <li><a href="electrostaticembed.html#module-quippy.electrostaticembed">quippy.electrostaticembed (module)</a>
</li>
      <li><a href="farray.html#module-quippy.farray">quippy.farray (module)</a>
</li>
      <li><a href="find_surface_atoms.html#module-quippy.find_surface_atoms">quippy.find_surface_atoms (module)</a>
</li>
      <li><a href="fortranio.html#module-quippy.fortranio">quippy.fortranio (module)</a>
</li>
      <li><a href="io.html#module-quippy.imd">quippy.imd (module)</a>
</li>
      <li><a href="io.html#module-quippy.io">quippy.io (module)</a>
</li>
      <li><a href="linearalgebra.html#module-quippy.linearalgebra">quippy.linearalgebra (module)</a>
</li>
      <li><a href="lotf.html#module-quippy.lotf">quippy.lotf (module)</a>
</li>
      <li><a href="mpi_context.html#module-quippy.mpi_context">quippy.mpi_context (module)</a>
</li>
      <li><a href="io.html#module-quippy.netcdf">quippy.netcdf (module)</a>
</li>
      <li><a href="io.html#module-quippy.nmwiz">quippy.nmwiz (module)</a>
</li>
      <li><a href="oo_fortran.html#module-quippy.oo_fortran">quippy.oo_fortran (module)</a>
</li>
      <li><a href="paramreader.html#module-quippy.paramreader">quippy.paramreader (module)</a>
</li>
      <li><a href="periodictable.html#module-quippy.periodictable">quippy.periodictable (module)</a>
</li>
      <li><a href="phonons.html#module-quippy.phonons">quippy.phonons (module)</a>
</li>
      <li><a href="polarization.html#module-quippy.polarization">quippy.polarization (module)</a>
</li>
      <li><a href="potential.html#module-quippy.potential">quippy.potential (module)</a>
</li>
      <li><a href="io.html#module-quippy.povray">quippy.povray (module)</a>
</li>
      <li><a href="qpxml.html#module-quippy.qpxml">quippy.qpxml (module)</a>
</li>
      <li><a href="quaternions.html#module-quippy.quaternions">quippy.quaternions (module)</a>
</li>
      <li><a href="real_space_covariance.html#module-quippy.real_space_covariance">quippy.real_space_covariance (module)</a>
</li>
      <li><a href="simplex.html#module-quippy.simplex">quippy.simplex (module)</a>
</li>
      <li><a href="spline.html#module-quippy.spline">quippy.spline (module)</a>
</li>
      <li><a href="structures.html#module-quippy.structures">quippy.structures (module)</a>
</li>
      <li><a href="system.html#module-quippy.system">quippy.system (module)</a>
</li>
      <li><a href="table.html#module-quippy.table">quippy.table (module)</a>
</li>
      <li><a href="topology.html#module-quippy.topology">quippy.topology (module)</a>
</li>
      <li><a href="units.html#module-quippy.units">quippy.units (module)</a>
</li>
      <li><a href="util.html#module-quippy.util">quippy.util (module)</a>
</li>
      <li><a href="io.html#module-quippy.vasp">quippy.vasp (module)</a>
</li>
      <li><a href="qlab.html#qlab.QuippyViewer">QuippyViewer (class in qlab)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.r">r (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="system.html#quippy.system.ran">ran() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.ran_exp">ran_exp() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.ran_normal">ran_normal() (in module quippy.system)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.ran_normal3">ran_normal3() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="system.html#quippy.system.ran_string">ran_string() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.ran_uniform">ran_uniform() (in module quippy.system)</a>
</li>
      <li><a href="io.html#quippy.io.AtomsReader.random_access">random_access (quippy.io.AtomsReader attribute)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.random_quaternion">random_quaternion() (in module quippy.real_space_covariance)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.random_seed">random_seed (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.random_unit_vector">random_unit_vector() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.randomise">randomise() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.randomise">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.randomise">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.randomise">[3]</a>, <a href="linearalgebra.html#quippy.linearalgebra.randomise">[4]</a>, <a href="linearalgebra.html#quippy.linearalgebra.randomise">[5]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.rattle">rattle() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.rayleigh_wave_speed">rayleigh_wave_speed() (in module quippy.elasticity)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.rcut_patch">rcut_patch() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.rcut_patch">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.rcut_patch">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="io.html#quippy.io.read">read() (in module quippy.io)</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.read">(quippy.atoms.Atoms class method)</a>
</li>
        <li><a href="io.html#quippy.castep.CastepCell.read">(quippy.castep.CastepCell method)</a>
</li>
        <li><a href="io.html#quippy.castep.CastepParam.read">(quippy.castep.CastepParam method)</a>
</li>
        <li><a href="io.html#quippy.cinoutput.CInOutput.read">(quippy.cinoutput.CInOutput method)</a>
</li>
        <li><a href="potential.html#quippy.potential.Potential.read">(quippy.potential.Potential method)</a>
</li>
      </ul></li>
      <li><a href="system.html#quippy.system.InOutput.read_ascii">read_ascii() (quippy.system.InOutput method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.read_cinoutput">read_cinoutput() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k.read_cp2k_qm_kind">read_cp2k_qm_kind() (in module quippy.cp2k)</a>
</li>
      <li><a href="io.html#quippy.io.read_dataset">read_dataset() (in module quippy.io)</a>
</li>
      <li><a href="f90doc.html#f90doc.read_files">read_files() (in module f90doc)</a>
</li>
      <li><a href="io.html#quippy.castep.read_formatted_density">read_formatted_density() (in module quippy.castep)</a>
</li>
      <li><a href="io.html#quippy.castep.read_formatted_potential">read_formatted_potential() (in module quippy.castep)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.read_from">read_from() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="io.html#quippy.castep.CastepParam.read_from_castep_output">read_from_castep_output() (quippy.castep.CastepParam method)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.read_line">read_line() (quippy.system.InOutput method)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k_driver.read_output">read_output() (in module quippy.cp2k_driver)</a>
</li>
      <li><a href="cp2k.html#quippy.cp2k.read_psf">read_psf() (in module quippy.cp2k)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.read_string">read_string() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.read_xml">read_xml() (quippy.crack.CrackParams method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.real">real (quippy.table.Table attribute)</a>
</li>
      <li><a href="system.html#quippy.system.real_format_length">real_format_length() (in module quippy.system)</a>
</li>
      <li><a href="table.html#quippy.table.Table.real_part">real_part() (quippy.table.Table method)</a>
</li>
      <li><a href="system.html#quippy.system.real_sci_format_length">real_sci_format_length() (in module quippy.system)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.realpos">realpos() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.realsize">realsize (quippy.table.Table attribute)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance">RealSpaceCovariance (class in quippy.real_space_covariance)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.align">RealSpaceCovariance.align() (in module quippy.real_space_covariance)</a>, <a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.align">[1]</a>, <a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.align">[2]</a>
</li>
      <li><a href="table.html#quippy.table.Table.record_delete_multiple">record_delete_multiple() (quippy.table.Table method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.recv_l">recv_l (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.recv_r">recv_r (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.redraw">redraw() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.redraw">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.redraw">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.ref_count">ref_count (quippy.atoms.Atoms attribute)</a>
</li>
      <li><a href="system.html#quippy.system.reference_false">reference_false() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.reference_true">reference_true() (in module quippy.system)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.remove_atoms">remove_atoms() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.remove_atoms">(quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      </ul></li>
      <li><a href="connection.html#quippy.atoms.Connection.remove_bond">remove_bond() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.remove_bonds">remove_bonds() (quippy.atoms.Connection method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.remove_columns">remove_columns() (quippy.table.Table method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.remove_property">remove_property() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.remove_thermostat">remove_thermostat() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.remove_thermostat">(quippy.dynamicalsystem.Dynamics method)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.remove_too_close_atoms">remove_too_close_atoms() (in module quippy.structures)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.remove_value">remove_value() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="qlab.html#qlab.render_movie">render_movie() (in module qlab)</a>

      <ul>
        <li><a href="qlab.html#qlab.QuippyViewer.render_movie">(qlab.QuippyViewer method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.repeat">repeat() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.repoint">repoint() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.rescale_velo">rescale_velo() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.reset">reset() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.reset_aux_property_thresholds">reset_aux_property_thresholds() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.reset_aux_property_thresholds">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.reset_aux_property_thresholds">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.resize">resize() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.resize">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.resize">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.restore_state">restore_state() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.reverse_properties">reverse_properties (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="system.html#quippy.system.InOutput.rewind">rewind() (quippy.system.InOutput method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.rms_diff">rms_diff() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.rms_diff">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.rms_diff">[2]</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.rotate">rotate() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.rotate">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.rotate">(in module qlab)</a>
</li>
        <li><a href="quaternions.html#quippy.quaternions.rotate">(in module quippy.quaternions)</a>, <a href="quaternions.html#quippy.quaternions.rotate">[1]</a>, <a href="quaternions.html#quippy.quaternions.rotate">[2]</a>
</li>
        <li><a href="atoms.html#quippy.atoms.Atoms.rotate">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="quaternions.html#quippy.quaternions.Quaternion.rotate">(quippy.quaternions.Quaternion method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.rotate_dihedral">rotate_dihedral() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="quaternions.html#quippy.quaternions.Quaternion.rotate_quat">rotate_quat() (quippy.quaternions.Quaternion method)</a>
</li>
      <li><a href="quaternions.html#quippy.quaternions.rotation">rotation() (in module quippy.quaternions)</a>
</li>
      <li><a href="structures.html#quippy.structures.rotation_matrix">rotation_matrix() (in module quippy.structures)</a>

      <ul>
        <li><a href="quaternions.html#quippy.quaternions.Quaternion.rotation_matrix">(quippy.quaternions.Quaternion method)</a>
</li>
      </ul></li>
      <li><a href="quaternions.html#quippy.quaternions.Quaternion.rotation_parameters">rotation_parameters() (quippy.quaternions.Quaternion method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.rotmat_quaternion">rotmat_quaternion() (in module quippy.real_space_covariance)</a>
</li>
      <li><a href="system.html#quippy.system.round">round() (in module quippy.system)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.round_prime_factors">round_prime_factors() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.row_iter">row_iter() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.rows">rows (quippy.farray.FortranArray attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.run">run() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.run">(quippy.dynamicalsystem.Dynamics method)</a>
</li>
        <li><a href="lotf.html#quippy.lotf.LOTFDynamics.run">(quippy.lotf.LOTFDynamics method)</a>
</li>
        <li><a href="potential.html#quippy.potential.Minim.run">(quippy.potential.Minim method)</a>
</li>
      </ul></li>
      <li><a href="io.html#quippy.castep.run_castep">run_castep() (in module quippy.castep)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.run_command">run_command() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.run_command">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.run_command">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.run_script">run_script() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.run_script">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.run_script">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.rutile">rutile() (in module quippy.structures)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="system.html#quippy.system.s2a">s2a() (in module quippy.system)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.save">save() (atomeye.AtomEyeViewer method)</a>
</li>
      <li><a href="atomeye.html#atomeye.save_script">save_script() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.save_script">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.save_state">save_state() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.scalar_triple_product">scalar_triple_product() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.scat">scat() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="qlab.html#qlab.AtomsViewer.scat">(qlab.AtomsViewer method)</a>
</li>
      </ul></li>
      <li><a href="polarization.html#quippy.polarization.screened_effective_charge">screened_effective_charge() (in module quippy.polarization)</a>
</li>
      <li><a href="qlab.html#qlab.scv">scv() (in module qlab)</a>
</li>
      <li><a href="table.html#quippy.table.Table.search">search() (quippy.table.Table method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.select">select() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="table.html#quippy.table.Table.select">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="qlab.html#qlab.select_atoms">select_atoms() (in module qlab)</a>

      <ul>
        <li><a href="qlab.html#qlab.QuippyViewer.select_atoms">(qlab.QuippyViewer method)</a>
</li>
      </ul></li>
      <li><a href="crack.html#quippy.crack.select_ellipse">select_ellipse() (in module quippy.crack)</a>
</li>
      <li><a href="atomeye.html#atomeye.select_gear">select_gear() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.select_gear">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_cutoff_plane">selection_cutoff_plane (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_directionality">selection_directionality (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_edge_tol">selection_edge_tol (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_ellipse">selection_ellipse (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_ellipse_bias">selection_ellipse_bias (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_ellipse_buffer">selection_ellipse_buffer (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_max_qm_atoms">selection_max_qm_atoms (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_method">selection_method (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.selection_update_interval">selection_update_interval (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.send_l">send_l (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.send_r">send_r (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.sendrecv">sendrecv() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.set">set() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_angle">set_angle() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_array">set_array() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_atomic_numbers">set_atomic_numbers() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_atoms">set_atoms() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.set_barostat">set_barostat() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.set_barostat">(quippy.dynamicalsystem.Dynamics method)</a>
</li>
      </ul></li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.set_border">set_border() (quippy.atoms.DomainDecomposition method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.set_calc_args">set_calc_args() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_calculator">set_calculator() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.set_callback">set_callback() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_cell">set_cell() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_celldisp">set_celldisp() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_chemical_symbols">set_chemical_symbols() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_comm_property">set_comm_property() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.set_comm_property">(quippy.atoms.DomainDecomposition method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_constraint">set_constraint() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_cutoff">set_cutoff() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_cutoff_minimum">set_cutoff_minimum() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="qlab.html#qlab.set_cutoffs">set_cutoffs() (in module qlab)</a>

      <ul>
        <li><a href="qlab.html#qlab.QuippyViewer.set_cutoffs">(qlab.QuippyViewer method)</a>
</li>
      </ul></li>
      <li><a href="potential.html#quippy.potential.Potential.set_default_properties">set_default_properties() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atomeye.html#atomeye.set_delta">set_delta() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.set_delta">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_dihedral">set_dihedral() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_distance">set_distance() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.set_frame">set_frame() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.set_frame">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="table.html#quippy.table.Table.set_increment">set_increment() (quippy.table.Table method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_initial_charges">set_initial_charges() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_initial_magnetic_moments">set_initial_magnetic_moments() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.set_label">set_label() (quippy.potential.Potential method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_lattice">set_lattice() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_map_shift">set_map_shift() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_masses">set_masses() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="qpxml.html#quippy.qpxml.set_max_gap_version">set_max_gap_version() (in module quippy.qpxml)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_momenta">set_momenta() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.set_n">set_n() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_param_value">set_param_value() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_pbc">set_pbc() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_positions">set_positions() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="potential.html#quippy.potential.ForceMixingPotential.set_qm_atoms">set_qm_atoms() (quippy.potential.ForceMixingPotential method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.set_qm_update_func">set_qm_update_func() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_scaled_positions">set_scaled_positions() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.set_state">set_state() (quippy.lotf.LOTFDynamics method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_tags">set_tags() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.set_temperature">set_temperature() (quippy.dynamicalsystem.Dynamics method)</a>
</li>
      <li><a href="system.html#quippy.system.set_timing">set_timing() (in module quippy.system)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.set_value">set_value() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.set_value_pointer">set_value_pointer() (quippy.dictionary.Dictionary method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_velocities">set_velocities() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.set_zs">set_zs() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.setp">setp() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.setp">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.setp">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="potential.html#quippy.potential.Potential.setup_parallel">setup_parallel() (quippy.potential.Potential method)</a>
</li>
      <li><a href="structures.html#quippy.structures.sh">sh() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.sh2">sh2() (in module quippy.structures)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType.shallow_copy">shallow_copy() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.FortranDerivedType.shallow_copy_from">shallow_copy_from() (quippy.oo_fortran.FortranDerivedType method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.shift_cutting_plane">shift_cutting_plane() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.shift_cutting_plane">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.shift_cutting_plane">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.shift_cutting_plane_to_anchor">shift_cutting_plane_to_anchor() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.shift_cutting_plane_to_anchor">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.shift_xtal">shift_xtal() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.shift_xtal">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.shift_xtal">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.show">show() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="qlab.html#qlab.QuippyViewer.show">(qlab.QuippyViewer method)</a>
</li>
      </ul></li>
      <li><a href="atoms.html#quippy.atoms.Atoms.shuffle">shuffle() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.sign">sign() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.sign">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.sign">[2]</a>
</li>
      <li><a href="structures.html#quippy.structures.MillerIndex.simplify">simplify() (quippy.structures.MillerIndex method)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.simulation_classical">simulation_classical (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.simulation_force_initial_load_step">simulation_force_initial_load_step (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.simulation_initial_state">simulation_initial_state (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.simulation_seed">simulation_seed (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.CrackParams.simulation_task">simulation_task (quippy.crack.CrackParams attribute)</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Descriptor.sizes">sizes() (quippy.descriptors.Descriptor method)</a>

      <ul>
        <li><a href="descriptors.html#quippy.descriptors.General_monomer.sizes">(quippy.descriptors.General_monomer method)</a>
</li>
        <li><a href="descriptors.html#quippy.descriptors.Soap.sizes">(quippy.descriptors.Soap method)</a>
</li>
      </ul></li>
      <li><a href="structures.html#quippy.structures.slab">slab() (in module quippy.structures)</a>, <a href="structures.html#quippy.structures.slab">[1]</a>, <a href="structures.html#quippy.structures.slab">[2]</a>
</li>
      <li><a href="descriptors.html#quippy.descriptors.Soap">Soap (class in quippy.descriptors)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.sort">sort() (quippy.atoms.Atoms method)</a>

      <ul>
        <li><a href="io.html#quippy.io.AtomsList.sort">(quippy.io.AtomsList method)</a>
</li>
        <li><a href="table.html#quippy.table.Table.sort">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.sort_array">sort_array() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.sort_array">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.sort_array">[2]</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.sort_by_rindex">sort_by_rindex() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline">Spline (class in quippy.spline)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.split_context">split_context() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="system.html#quippy.system.split_string">split_string() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.split_string_simple">split_string_simple() (in module quippy.system)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.start">start() (atomeye.AtomEyeViewer method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.state">state (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="lotf.html#quippy.lotf.LOTFDynamics.state_label">state_label (quippy.lotf.LOTFDynamics attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.step">step() (quippy.dynamicalsystem.Dynamics method)</a>

      <ul>
        <li><a href="lotf.html#quippy.lotf.LOTFDynamics.step">(quippy.lotf.LOTFDynamics method)</a>
</li>
      </ul></li>
      <li><a href="table.html#quippy.table.Table.str">str (quippy.table.Table attribute)</a>
</li>
      <li><a href="table.html#quippy.table.Table.str_part">str_part() (quippy.table.Table method)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.strain_matrix">strain_matrix() (in module quippy.elasticity)</a>
</li>
      <li><a href="crack.html#quippy.crack.strain_to_G">strain_to_G() (in module quippy.crack)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.strain_vector">strain_vector() (in module quippy.elasticity)</a>
</li>
      <li><a href="crack.html#quippy.crack.stress_intensity_factor">stress_intensity_factor() (in module quippy.crack)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.stress_matrix">stress_matrix() (in module quippy.elasticity)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.stress_vector">stress_vector() (in module quippy.elasticity)</a>
</li>
      <li><a href="system.html#quippy.system.string_to_int">string_to_int() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.string_to_logical">string_to_logical() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.string_to_numerical">string_to_numerical() (in module quippy.system)</a>, <a href="system.html#quippy.system.string_to_numerical">[1]</a>, <a href="system.html#quippy.system.string_to_numerical">[2]</a>, <a href="system.html#quippy.system.string_to_numerical">[3]</a>, <a href="system.html#quippy.system.string_to_numerical">[4]</a>, <a href="system.html#quippy.system.string_to_numerical">[5]</a>, <a href="system.html#quippy.system.string_to_numerical">[6]</a>
</li>
      <li><a href="system.html#quippy.system.string_to_real">string_to_real() (in module quippy.system)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.stripstrings">stripstrings() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.strsize">strsize (quippy.table.Table attribute)</a>
</li>
      <li><a href="structures.html#quippy.structures.structure_from_file">structure_from_file() (in module quippy.structures)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.subset">subset() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="table.html#quippy.table.Table.subtable">subtable() (quippy.table.Table method)</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.sum">sum() (quippy.farray.FortranArray method)</a>

      <ul>
        <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.sum">(quippy.mpi_context.MPI_context method)</a>
</li>
      </ul></li>
      <li><a href="qpxml.html#quippy.qpxml.sum_e0">sum_e0() (in module quippy.qpxml)</a>
</li>
      <li><a href="mpi_context.html#quippy.mpi_context.MPI_context.sum_in_place">sum_in_place() (quippy.mpi_context.MPI_context method)</a>
</li>
      <li><a href="structures.html#quippy.structures.supercell">supercell() (in module quippy.structures)</a>
</li>
      <li><a href="structures.html#quippy.structures.surface_unit_cell">surface_unit_cell() (in module quippy.structures)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.svdfact">svdfact() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.swap">swap() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.symmetric_linear_solve">symmetric_linear_solve() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.symmetrise">symmetrise() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.symmetrise">[1]</a>
</li>
      <li><a href="system.html#quippy.system.system_finalise">system_finalise() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.system_get_random_seed">system_get_random_seed() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.system_initialise">system_initialise() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.system_reseed_rng">system_reseed_rng() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.system_resync_rng">system_resync_rng() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.system_set_random_seeds">system_set_random_seeds() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.system_timer">system_timer() (in module quippy.system)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.t">t (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="table.html#quippy.table.Table">Table (class in quippy.table)</a>
</li>
      <li><a href="table.html#quippy.table.Table.append">Table.append() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.append">[1]</a>, <a href="table.html#quippy.table.Table.append">[2]</a>, <a href="table.html#quippy.table.Table.append">[3]</a>, <a href="table.html#quippy.table.Table.append">[4]</a>, <a href="table.html#quippy.table.Table.append">[5]</a>, <a href="table.html#quippy.table.Table.append">[6]</a>, <a href="table.html#quippy.table.Table.append">[7]</a>, <a href="table.html#quippy.table.Table.append">[8]</a>, <a href="table.html#quippy.table.Table.append">[9]</a>, <a href="table.html#quippy.table.Table.append">[10]</a>, <a href="table.html#quippy.table.Table.append">[11]</a>, <a href="table.html#quippy.table.Table.append">[12]</a>
</li>
      <li><a href="table.html#quippy.table.Table.append_column">Table.append_column() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.append_column">[1]</a>, <a href="table.html#quippy.table.Table.append_column">[2]</a>, <a href="table.html#quippy.table.Table.append_column">[3]</a>, <a href="table.html#quippy.table.Table.append_column">[4]</a>, <a href="table.html#quippy.table.Table.append_column">[5]</a>, <a href="table.html#quippy.table.Table.append_column">[6]</a>, <a href="table.html#quippy.table.Table.append_column">[7]</a>, <a href="table.html#quippy.table.Table.append_column">[8]</a>
</li>
      <li><a href="table.html#quippy.table.Table.delete">Table.delete() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.delete">[1]</a>
</li>
      <li><a href="table.html#quippy.table.Table.find">Table.find() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.find">[1]</a>
</li>
      <li><a href="table.html#quippy.table.Table.int_part">Table.int_part() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.int_part">[1]</a>, <a href="table.html#quippy.table.Table.int_part">[2]</a>
</li>
      <li><a href="table.html#quippy.table.Table.logical_part">Table.logical_part() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.logical_part">[1]</a>, <a href="table.html#quippy.table.Table.logical_part">[2]</a>
</li>
      <li><a href="table.html#quippy.table.Table.print">Table.print() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.print">[1]</a>
</li>
      <li><a href="table.html#quippy.table.Table.real_part">Table.real_part() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.real_part">[1]</a>, <a href="table.html#quippy.table.Table.real_part">[2]</a>
</li>
      <li><a href="table.html#quippy.table.Table.str_part">Table.str_part() (in module quippy.table)</a>, <a href="table.html#quippy.table.Table.str_part">[1]</a>, <a href="table.html#quippy.table.Table.str_part">[2]</a>
</li>
      <li><a href="farray.html#quippy.farray.FortranArray.take">take() (quippy.farray.FortranArray method)</a>
</li>
      <li><a href="real_space_covariance.html#quippy.real_space_covariance.RealSpaceCovariance.teach">teach() (quippy.real_space_covariance.RealSpaceCovariance method)</a>
</li>
      <li><a href="teach_sparse.html#quippy.teach_sparse_parse_command_line">teach_sparse_parse_command_line() (in module quippy)</a>
</li>
      <li><a href="teach_sparse.html#quippy.teach_sparse_parse_gap_str">teach_sparse_parse_gap_str() (in module quippy)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.temperature">temperature (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.temperature">temperature() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.termination_bond_rescale">termination_bond_rescale() (in module quippy.atoms)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.test_gradient">test_gradient() (quippy.potential.Potential method)</a>
</li>
      <li><a href="potential.html#quippy.potential.Potential.test_local_virial">test_local_virial() (quippy.potential.Potential method)</a>
</li>
      <li><a href="system.html#quippy.system.th">th() (in module quippy.system)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.thermostat_dw">thermostat_dw (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.thermostat_temperatures">thermostat_temperatures() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.thermostat_work">thermostat_work (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="crack.html#quippy.crack.thin_strip_displacement_y">thin_strip_displacement_y() (in module quippy.crack)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.time">time (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="util.html#quippy.util.time_ordered_glob">time_ordered_glob() (in module quippy.util)</a>
</li>
      <li><a href="io.html#quippy.io.time_ordered_series">time_ordered_series() (in module quippy.io)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.timestep">timestep (quippy.dynamicalsystem.Dynamics attribute)</a>
</li>
      <li><a href="table.html#quippy.table.Table.to_atom_list">to_atom_list() (quippy.table.Table method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="table.html#quippy.table.Table.to_atom_mask">to_atom_mask() (quippy.table.Table method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.toggle_aux_property_thresholds_rigid">toggle_aux_property_thresholds_rigid() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.toggle_aux_property_thresholds_rigid">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.toggle_aux_property_thresholds_rigid">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.toggle_aux_property_thresholds_saturation">toggle_aux_property_thresholds_saturation() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.toggle_aux_property_thresholds_saturation">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.toggle_aux_property_thresholds_saturation">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.toggle_bond_mode">toggle_bond_mode() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.toggle_bond_mode">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.toggle_bond_mode">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.toggle_coordination_coloring">toggle_coordination_coloring() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.toggle_coordination_coloring">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.toggle_coordination_coloring">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.toggle_parallel_projection">toggle_parallel_projection() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.toggle_parallel_projection">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.toggle_parallel_projection">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.toggle_small_cell_mode">toggle_small_cell_mode() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.toggle_small_cell_mode">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.toggle_small_cell_mode">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.torque">torque() (in module quippy.dynamicalsystem)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.trace">trace() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.trace">[1]</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.trace_mult">trace_mult() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.trace_mult">[1]</a>
</li>
      <li><a href="structures.html#quippy.structures.transform">transform() (in module quippy.structures)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.transform_basis">transform_basis() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="elasticity.html#quippy.elasticity.transform_elasticity">transform_elasticity() (in module quippy.elasticity)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.translate">translate() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.translate">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.translate">(in module qlab)</a>
</li>
        <li><a href="atoms.html#quippy.atoms.Atoms.translate">(quippy.atoms.Atoms method)</a>
</li>
      </ul></li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.trapezoidintegral">trapezoidintegral() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="structures.html#quippy.structures.tube_radius">tube_radius() (in module quippy.structures)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.undo_com_motion">undo_com_motion() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.undo_pbc_jumps">undo_pbc_jumps() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.uniq">uniq() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.uniq">[1]</a>
</li>
      <li><a href="structures.html#quippy.structures.unit_slab">unit_slab() (in module quippy.structures)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.unit_vector">unit_vector() (in module quippy.linearalgebra)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.unskew_cell">unskew_cell() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.update">update() (atomeye.AtomEyeViewer method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.update_barostat">update_barostat() (quippy.dynamicalsystem.Dynamics method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.update_exponential_average">update_exponential_average() (in module quippy.linearalgebra)</a>, <a href="linearalgebra.html#quippy.linearalgebra.update_exponential_average">[1]</a>, <a href="linearalgebra.html#quippy.linearalgebra.update_exponential_average">[2]</a>, <a href="linearalgebra.html#quippy.linearalgebra.update_exponential_average">[3]</a>
</li>
      <li><a href="lotf.html#quippy.lotf.update_hysteretic_qm_region">update_hysteretic_qm_region() (in module quippy.lotf)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.update_thermostat">update_thermostat() (quippy.dynamicalsystem.DynamicalSystem method)</a>

      <ul>
        <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.Dynamics.update_thermostat">(quippy.dynamicalsystem.Dynamics method)</a>
</li>
      </ul></li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.upper">upper (quippy.atoms.DomainDecomposition attribute)</a>
</li>
      <li><a href="system.html#quippy.system.upper_case">upper_case() (in module quippy.system)</a>
</li>
      <li><a href="domaindecomposition.html#quippy.atoms.DomainDecomposition.upper_with_border">upper_with_border (quippy.atoms.DomainDecomposition attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="spline.html#quippy.spline.Spline.value">value() (quippy.spline.Spline method)</a>
</li>
      <li><a href="io.html#quippy.vasp.VASP_POSCAR_Reader">VASP_POSCAR_Reader() (in module quippy.vasp)</a>
</li>
      <li><a href="io.html#quippy.vasp.VASPWriter">VASPWriter (class in quippy.vasp)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.verbose">verbose (atomeye.AtomEyeViewer attribute)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_of_str">verbosity_of_str() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_pop">verbosity_pop() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_push">verbosity_push() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_push_decrement">verbosity_push_decrement() (in module quippy.system)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="system.html#quippy.system.verbosity_push_increment">verbosity_push_increment() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_set_minimum">verbosity_set_minimum() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_to_str">verbosity_to_str() (in module quippy.system)</a>
</li>
      <li><a href="system.html#quippy.system.verbosity_unset_minimum">verbosity_unset_minimum() (in module quippy.system)</a>
</li>
      <li><a href="atomeye.html#atomeye.view">view() (in module atomeye)</a>

      <ul>
        <li><a href="qlab.html#qlab.view">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="atomeye.html#atomeye.viewers">viewers (in module atomeye)</a>
</li>
      <li><a href="structures.html#quippy.structures.void_analysis">void_analysis() (in module quippy.structures)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="W">W</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.wait">wait() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.wait">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.wait">(in module qlab)</a>
</li>
      </ul></li>
      <li><a href="system.html#quippy.system.wait_for_file_to_exist">wait_for_file_to_exist() (in module quippy.system)</a>
</li>
      <li><a href="structures.html#quippy.structures.water">water() (in module quippy.structures)</a>
</li>
      <li><a href="connection.html#quippy.atoms.Connection.wipe">wipe() (quippy.atoms.Connection method)</a>

      <ul>
        <li><a href="table.html#quippy.table.Table.wipe">(quippy.table.Table method)</a>
</li>
      </ul></li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.wkin">wkin (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.work">work (quippy.dynamicalsystem.DynamicalSystem attribute)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.wrap">wrap() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="oo_fortran.html#quippy.oo_fortran.wrap_all">wrap_all() (in module quippy.oo_fortran)</a>
</li>
      <li><a href="f2py_wrapper_gen.html#f2py_wrapper_gen.wrap_mod">wrap_mod() (in module f2py_wrapper_gen)</a>
</li>
      <li><a href="io.html#quippy.io.write">write() (in module quippy.io)</a>

      <ul>
        <li><a href="atoms.html#quippy.atoms.Atoms.write">(quippy.atoms.Atoms method)</a>
</li>
        <li><a href="io.html#quippy.castep.CastepCell.write">(quippy.castep.CastepCell method)</a>
</li>
        <li><a href="io.html#quippy.castep.CastepParam.write">(quippy.castep.CastepParam method)</a>
</li>
        <li><a href="io.html#quippy.cinoutput.CInOutput.write">(quippy.cinoutput.CInOutput method)</a>
</li>
        <li><a href="io.html#quippy.nmwiz.NMDWriter.write">(quippy.nmwiz.NMDWriter method)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="topology.html#quippy.topology.write_brookhaven_pdb_file">write_brookhaven_pdb_file() (in module quippy.topology)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.write_cinoutput">write_cinoutput() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="topology.html#quippy.topology.write_cp2k_pdb_file">write_cp2k_pdb_file() (in module quippy.topology)</a>
</li>
      <li><a href="topology.html#quippy.topology.write_psf_file">write_psf_file() (in module quippy.topology)</a>
</li>
      <li><a href="topology.html#quippy.topology.write_psf_file_arb_pos">write_psf_file_arb_pos() (in module quippy.topology)</a>
</li>
      <li><a href="dictionary.html#quippy.dictionary.Dictionary.write_string">write_string() (quippy.dictionary.Dictionary method)</a>
</li>
      <li><a href="util.html#quippy.util.write_timings">write_timings() (in module quippy.util)</a>
</li>
      <li><a href="structures.html#quippy.structures.wurtzite">wurtzite() (in module quippy.structures)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="X">X</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="spline.html#quippy.spline.Spline.x">x (quippy.spline.Spline attribute)</a>
</li>
      <li><a href="atomeye.html#atomeye.AtomEyeViewer.xtal_origin_goto">xtal_origin_goto() (atomeye.AtomEyeViewer method)</a>

      <ul>
        <li><a href="atomeye.html#atomeye.xtal_origin_goto">(in module atomeye)</a>
</li>
        <li><a href="qlab.html#qlab.xtal_origin_goto">(in module qlab)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="Y">Y</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="spline.html#quippy.spline.Spline.y">y (quippy.spline.Spline attribute)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline.y2">y2 (quippy.spline.Spline attribute)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="elasticity.html#quippy.elasticity.youngs_modulus">youngs_modulus() (in module quippy.elasticity)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline.yp1">yp1 (quippy.spline.Spline attribute)</a>
</li>
      <li><a href="spline.html#quippy.spline.Spline.ypn">ypn (quippy.spline.Spline attribute)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Z">Z</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.z_index_to_index">z_index_to_index() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="atoms.html#quippy.atoms.Atoms.zero">zero() (quippy.atoms.Atoms method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="atoms.html#quippy.atoms.Atoms.zero_angular_momentum">zero_angular_momentum() (quippy.atoms.Atoms method)</a>
</li>
      <li><a href="dynamicalsystem.html#quippy.dynamicalsystem.DynamicalSystem.zero_momentum">zero_momentum() (quippy.dynamicalsystem.DynamicalSystem method)</a>
</li>
      <li><a href="linearalgebra.html#quippy.linearalgebra.zero_sum">zero_sum() (in module quippy.linearalgebra)</a>
</li>
  </ul></td>
</tr></table>



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